From b9ecce086c3ff895ac0e42581c9134e5247c46f1 Mon Sep 17 00:00:00 2001 From: melferink Date: Thu, 25 May 2023 08:21:31 +0200 Subject: [PATCH 01/15] first commit --- Tracks/SureSelect_CREv4_elidS34226467_Covered.list | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 Tracks/SureSelect_CREv4_elidS34226467_Covered.list diff --git a/Tracks/SureSelect_CREv4_elidS34226467_Covered.list b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list new file mode 100644 index 0000000..a6e8c87 --- /dev/null +++ b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d0d5c43e62f92f2827c486b01ac872b3f61582fbfad05de1d3f1092525bcdf39 +size 6682248 From fac95fd4018eb742cc45d5770bf8746bf08a0cc1 Mon Sep 17 00:00:00 2001 From: melferink Date: Thu, 25 May 2023 10:06:22 +0200 Subject: [PATCH 02/15] update for calling target for CREv4 design --- Tracks/README.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/Tracks/README.md b/Tracks/README.md index 3c73076..8095837 100644 --- a/Tracks/README.md +++ b/Tracks/README.md @@ -39,3 +39,31 @@ java -jar -Xmx4G picard.jar BedToIntervalList I=ENSEMBL_UCSC_merged_collapsed_so rm S31285117_Padded_nochr.bed S31285117_Padded_nochr_unique.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank_tmp.bed ``` +### __25-05-2023. Addition of Agilent SureSelect CREv4 specific targets to the calling target.__ + +Requirements: +* Original target BED file (i.e. ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.bed ). +* Track files from Agilent SureSelect CREv4 elidS34226467 specifically the Padded.ped track. Files can be downloaded from the Agilent website. Make sure padded file has 100bp extensions. In case op CREv4 this is 50bp, so target needs to be extended. +* Dictionary from reference genome (same hg version), i.e. Homo_sapiens.GRCh37.GATK.illumina.dict +* Image of Bedtools software (tested v2.25.0) +* Image of Picard software (tested v1.140 and above) + +``` +# Extend padded flanks to 100bp and merge overlapping targets. Fix negative values and longer than MT length. +grep -vE "^browser|^track" S34226467_Padded.bed | sed 's/^chr//g' | sed 's/^M/MT/g' | awk '{OFS ="\t"; print $1,$2-50,$3+50}' | awk '{OFS="\t"; if ($2 < 0) print $1, 0, $3 ; else print $0}' |awk '{OFS="\t"; if ($1 == "MT" && $3> 16569) print $1,$2,16569; else print $0}' | sort -k 1V -k 2n -k 3n > S34226467_Padded_100bp.bed +singularity run -B /hpc/:/hpc/ -B $TMPDIR:$TMPDIR /hpc/diaggen/software/singularity_cache/quay.io-biocontainers-bedtools-2.25.0--he860b03_5.img +bedtools merge -i S34226467_Padded_100bp.bed | awk '{OFS ="\t"; print $1,$2,$3,"+","crev4_target","crev4_target","crev4_target"}' > S34226467_Padded_100bp_5kol.bed +bedtools subtract -a S34226467_Padded_100bp_5kol.bed -b ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.bed > S34226467_Padded_unique.bed +exit + +cat ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.bed S34226467_Padded_unique.bed |sed 's/^MT/Z/g'| sort -k1,1V -nk2 -nk3 | sed 's/^Z/MT/g' > ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed + +cat ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed | cut -f1,2,3,5 > ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank_tmp.bed + +singularity run -B /hpc/:/hpc/ -B $TMPDIR:$TMPDIR /hpc/diaggen/software/singularity_cache/quay.io-biocontainers-picard-3.0.0--hdfd78af_1.img +picard -Xmx4G BedToIntervalList I=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank_tmp.bed O=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list UNIQUE=true SD=/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.dict +exit + +rm S34226467_Padded.bed S34226467_Padded_unique.bed S34226467_Padded_100bp_5kol.bed S34226467_Padded_100bp.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank_tmp.bed +``` + From 2e5d8125efbcf501099fd312ad7ca010231b4e6b Mon Sep 17 00:00:00 2001 From: melferink Date: Thu, 25 May 2023 10:10:57 +0200 Subject: [PATCH 03/15] first commit --- ..._merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed diff --git a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed new file mode 100644 index 0000000..54d369c --- /dev/null +++ b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:40092e99e486810fac43451ec8f875c5da7415caa018d4ffb305d973af089142 +size 61595599 From 7ecb78045ab86b0d26044277cba6fc6feab351ab Mon Sep 17 00:00:00 2001 From: melferink Date: Thu, 25 May 2023 10:11:03 +0200 Subject: [PATCH 04/15] first commit --- ...llapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list diff --git a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list new file mode 100644 index 0000000..1a84d45 --- /dev/null +++ b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1f9b1677a5d70356905e21295077279922ec66005bb1c4c0fabb0fea4d8bbf75 +size 10616548 From 0257219a90615bfd3e2be6c5fd2e8b92d0fdb1a5 Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 26 Jun 2023 11:41:31 +0200 Subject: [PATCH 05/15] fixed file format mistake --- Tracks/SureSelect_CREv4_elidS34226467_Covered.list | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Tracks/SureSelect_CREv4_elidS34226467_Covered.list b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list index a6e8c87..73f4b5e 100644 --- a/Tracks/SureSelect_CREv4_elidS34226467_Covered.list +++ b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d0d5c43e62f92f2827c486b01ac872b3f61582fbfad05de1d3f1092525bcdf39 -size 6682248 +oid sha256:56fe732fd2b8c389f06d00a6f05d2958e838dc7b86a3deb9b1486f6ff1675d94 +size 5757248 From e907a6ac14f0b2c9cd0b1bf83ff89780eb56dcd1 Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 26 Jun 2023 17:15:19 +0200 Subject: [PATCH 06/15] change M to MT, and fixed 0-offset of MT target --- Tracks/SureSelect_CREv4_elidS34226467_Covered.list | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Tracks/SureSelect_CREv4_elidS34226467_Covered.list b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list index 73f4b5e..0ae73de 100644 --- a/Tracks/SureSelect_CREv4_elidS34226467_Covered.list +++ b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:56fe732fd2b8c389f06d00a6f05d2958e838dc7b86a3deb9b1486f6ff1675d94 -size 5757248 +oid sha256:60ce9f5950a475e3c4e22cc5ff9cfdb14d1ebf3bbd577428c0e1b7641275a0e8 +size 5757254 From 32e75959c5e17c41ae88660518b6b62d25ee150c Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 10:59:06 +0200 Subject: [PATCH 07/15] included additional regions --- Tracks/README.md | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/Tracks/README.md b/Tracks/README.md index 8095837..18abe63 100644 --- a/Tracks/README.md +++ b/Tracks/README.md @@ -43,13 +43,15 @@ rm S31285117_Padded_nochr.bed S31285117_Padded_nochr_unique.bed ENSEMBL_UCSC_mer Requirements: * Original target BED file (i.e. ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.bed ). -* Track files from Agilent SureSelect CREv4 elidS34226467 specifically the Padded.ped track. Files can be downloaded from the Agilent website. Make sure padded file has 100bp extensions. In case op CREv4 this is 50bp, so target needs to be extended. +* Track files from Agilent SureSelect CREv4 elidS34226467 specifically the Padded.ped track. Files can be downloaded from the Agilent website. Make sure padded file has 100bp extensions. In case of CREv4 this is 50bp, so target needs to be extended. * Dictionary from reference genome (same hg version), i.e. Homo_sapiens.GRCh37.GATK.illumina.dict * Image of Bedtools software (tested v2.25.0) * Image of Picard software (tested v1.140 and above) ``` # Extend padded flanks to 100bp and merge overlapping targets. Fix negative values and longer than MT length. +# In addition extra regions have been included as requested by BvZ: file additional_regions.bed + grep -vE "^browser|^track" S34226467_Padded.bed | sed 's/^chr//g' | sed 's/^M/MT/g' | awk '{OFS ="\t"; print $1,$2-50,$3+50}' | awk '{OFS="\t"; if ($2 < 0) print $1, 0, $3 ; else print $0}' |awk '{OFS="\t"; if ($1 == "MT" && $3> 16569) print $1,$2,16569; else print $0}' | sort -k 1V -k 2n -k 3n > S34226467_Padded_100bp.bed singularity run -B /hpc/:/hpc/ -B $TMPDIR:$TMPDIR /hpc/diaggen/software/singularity_cache/quay.io-biocontainers-bedtools-2.25.0--he860b03_5.img bedtools merge -i S34226467_Padded_100bp.bed | awk '{OFS ="\t"; print $1,$2,$3,"+","crev4_target","crev4_target","crev4_target"}' > S34226467_Padded_100bp_5kol.bed @@ -58,12 +60,16 @@ exit cat ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_100bpflank.bed S34226467_Padded_unique.bed |sed 's/^MT/Z/g'| sort -k1,1V -nk2 -nk3 | sed 's/^Z/MT/g' > ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed -cat ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed | cut -f1,2,3,5 > ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank_tmp.bed +cat ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed additional_regions.bed | sed 's/^MT/Z/g'| sort -k1,1V -nk2 -nk3 | sed 's/^Z/MT/g' > ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed + + + +cat ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed | cut -f1,2,3,5 > ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank_tmp.bed singularity run -B /hpc/:/hpc/ -B $TMPDIR:$TMPDIR /hpc/diaggen/software/singularity_cache/quay.io-biocontainers-picard-3.0.0--hdfd78af_1.img -picard -Xmx4G BedToIntervalList I=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank_tmp.bed O=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list UNIQUE=true SD=/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.dict +picard -Xmx4G BedToIntervalList I=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank_tmp.bed O=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list UNIQUE=true SD=/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.dict exit -rm S34226467_Padded.bed S34226467_Padded_unique.bed S34226467_Padded_100bp_5kol.bed S34226467_Padded_100bp.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank_tmp.bed +rm S34226467_Padded.bed S34226467_Padded_unique.bed S34226467_Padded_100bp_5kol.bed S34226467_Padded_100bp.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank_tmp.bed ``` From 4a1ea233f1ae506f3b2dee16488dcad6caec6d01 Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 10:59:41 +0200 Subject: [PATCH 08/15] update --- Tracks/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Tracks/README.md b/Tracks/README.md index 18abe63..be37e0b 100644 --- a/Tracks/README.md +++ b/Tracks/README.md @@ -70,6 +70,6 @@ singularity run -B /hpc/:/hpc/ -B $TMPDIR:$TMPDIR /hpc/diaggen/software/singular picard -Xmx4G BedToIntervalList I=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank_tmp.bed O=ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list UNIQUE=true SD=/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.dict exit -rm S34226467_Padded.bed S34226467_Padded_unique.bed S34226467_Padded_100bp_5kol.bed S34226467_Padded_100bp.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank_tmp.bed +rm S34226467_Padded.bed S34226467_Padded_unique.bed S34226467_Padded_100bp_5kol.bed S34226467_Padded_100bp.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank_tmp.bed ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed ``` From 6698a36ade5d519253e5697227e79a436d721171 Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 11:01:47 +0200 Subject: [PATCH 09/15] removed --- ..._merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed diff --git a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed deleted file mode 100644 index 54d369c..0000000 --- a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:40092e99e486810fac43451ec8f875c5da7415caa018d4ffb305d973af089142 -size 61595599 From 411d601f5aaf45d8811b2330f2db2cbd9cc84b49 Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 11:01:52 +0200 Subject: [PATCH 10/15] removed --- ...llapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list diff --git a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list deleted file mode 100644 index 1a84d45..0000000 --- a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.interval_list +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1f9b1677a5d70356905e21295077279922ec66005bb1c4c0fabb0fea4d8bbf75 -size 10616548 From 87287f3496614055a975642c39b77f263262a2bf Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 11:02:37 +0200 Subject: [PATCH 11/15] bed file with additional to-be-included regions --- Tracks/additional_regions.bed | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 Tracks/additional_regions.bed diff --git a/Tracks/additional_regions.bed b/Tracks/additional_regions.bed new file mode 100644 index 0000000..b61d2a8 --- /dev/null +++ b/Tracks/additional_regions.bed @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:232dc40037772cfcde20aeb4d9f1b4836216d137e9b73571cb7144819cbe6132 +size 72 From 764cea03f69c273d2356be8ea766438ccfc8dc24 Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 11:02:58 +0200 Subject: [PATCH 12/15] added CREv4 and additional regions --- ...ged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed diff --git a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed new file mode 100644 index 0000000..d85477f --- /dev/null +++ b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.bed @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ad0c31fe601d0cabca2aa660d5f655d57dcb4fed922248dbed9026fe0cbaae6a +size 61595671 From abcb7c643183e45cc2edac122e16f5dde27b3cab Mon Sep 17 00:00:00 2001 From: melferink Date: Mon, 21 Aug 2023 11:03:08 +0200 Subject: [PATCH 13/15] added CREv4 and additional regions --- ...sed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list diff --git a/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list new file mode 100644 index 0000000..3bb5225 --- /dev/null +++ b/Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:99817abb79db7d611117c45c034454477c9efb376c4ed9ebe1535b8dfbb94dfc +size 10616565 From a51d674d5822fb0956c16e0fe764f84ab264a4f7 Mon Sep 17 00:00:00 2001 From: melferink Date: Tue, 12 Sep 2023 09:12:15 +0200 Subject: [PATCH 14/15] new highconfident file CREv4 --- ExomeDepth/HC_CREv4-2023-1_exon.tsv | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 ExomeDepth/HC_CREv4-2023-1_exon.tsv diff --git a/ExomeDepth/HC_CREv4-2023-1_exon.tsv b/ExomeDepth/HC_CREv4-2023-1_exon.tsv new file mode 100644 index 0000000..4026eb2 --- /dev/null +++ b/ExomeDepth/HC_CREv4-2023-1_exon.tsv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b9701326d491933ba9abb91f3442bd529529bc8ea156fc04538039d8238cf9ab +size 9987918 From 6f36c2a1e20a33b4561d03d332ff239b45967491 Mon Sep 17 00:00:00 2001 From: melferink Date: Tue, 12 Sep 2023 09:12:24 +0200 Subject: [PATCH 15/15] new highconfident file CREv4 --- ExomeDepth/HC_CREv4-2023-1_target.bed | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 ExomeDepth/HC_CREv4-2023-1_target.bed diff --git a/ExomeDepth/HC_CREv4-2023-1_target.bed b/ExomeDepth/HC_CREv4-2023-1_target.bed new file mode 100644 index 0000000..8dfe194 --- /dev/null +++ b/ExomeDepth/HC_CREv4-2023-1_target.bed @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5427a2e53c255a8017607e89b59368c0df1c69aeb22856b226cad2c26e92da0c +size 4993946