Merge pull request #45 from UMCUGenetics/release/v1.8.0

v1.8.0
UMCUGenetics · Nov 7, 2023 · 887e7ae · 887e7ae
2 parents 6787416 + 92ca90e
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diff --git a/ExomeDepth/HC_CREv4-2023-1_exon.tsv b/ExomeDepth/HC_CREv4-2023-1_exon.tsv
diff --git a/ExomeDepth/HC_CREv4-2023-1_target.bed b/ExomeDepth/HC_CREv4-2023-1_target.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
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
diff --git a/Tracks/README.md b/Tracks/README.md
@@ -39,3 +39,37 @@ 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 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 
+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 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_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 ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_100bpflank.bed
+```
+
diff --git a/Tracks/SureSelect_CREv4_elidS34226467_Covered.list b/Tracks/SureSelect_CREv4_elidS34226467_Covered.list
diff --git a/Tracks/additional_regions.bed b/Tracks/additional_regions.bed