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copy over some additional test data files
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| ##fileformat=VCFv4.1 | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##fileDate=15082017_02h10m46s | ||
| ##source=SHAPEIT2.v837 | ||
| ##log_file=shapeit_15082017_02h10m46s_d9e4b88d-2500-460c-9753-e6c2ac3bcb15.log | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype"> | ||
| ##contig=<ID=22> | ||
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> | ||
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
| ##bcftools_viewVersion=1.6-49-ga2ffda9-dirty+htslib-1.7-1-gaf40c73 | ||
| ##bcftools_viewCommand=view --samples SS0012978,SS0012979,SS0013012 -r 22:16050115-16052271 -Oz -o snps.vcf.gz /storage/resources/datasets/SSC_SNP_v3/shapeit.chr22.with.ref.v3.vcf.gz; Date=Wed Jan 29 11:43:55 2020 | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SS0012978 SS0012979 SS0013012 | ||
| 22 16050115 22:16050115:G:A G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050213 22:16050213:C:T C T . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050527 22:16050527:C:A C A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050607 22:16050607:G:A G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050783 22:16050783:A:G A G . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050840 22:16050840:C:G C G . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050847 22:16050847:T:C T C . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16050984 rs188945759 C G . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051075 22:16051075:G:A G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051246 22:16051246:G:A G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051249 rs62224609 T C . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051477 rs192339082 C A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051493 22:16051493:G:A G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051564 22:16051564:T:C T C . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16051816 22:16051816:T:G T G . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16052032 22:16052032:G:A G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 | ||
| 22 16052080 rs4965031 G A . PASS AC=1;AN=6 GT 0|0 0|0 1|0 | ||
| 22 16052271 rs188996808 G A . PASS AC=0;AN=6 GT 0|0 0|0 0|0 |
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|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| ##fileformat=VCFv4.1 | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant"> | ||
| ##INFO=<ID=REF,Number=1,Type=Integer,Description="Reference copy number"> | ||
| ##INFO=<ID=REPID,Number=1,Type=String,Description="Repeat identifier as specified in the variant catalog"> | ||
| ##INFO=<ID=RL,Number=1,Type=Integer,Description="Reference length in bp"> | ||
| ##INFO=<ID=RU,Number=1,Type=String,Description="Repeat unit in the reference orientation"> | ||
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | ||
| ##INFO=<ID=VARID,Number=1,Type=String,Description="Variant identifier as specified in the variant catalog"> | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##FORMAT=<ID=ADFL,Number=1,Type=String,Description="Number of flanking reads consistent with the allele"> | ||
| ##FORMAT=<ID=ADIR,Number=1,Type=String,Description="Number of in-repeat reads consistent with the allele"> | ||
| ##FORMAT=<ID=ADSP,Number=1,Type=String,Description="Number of spanning reads consistent with the allele"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=LC,Number=1,Type=Float,Description="Locus coverage"> | ||
| ##FORMAT=<ID=REPCI,Number=1,Type=String,Description="Confidence interval for REPCN"> | ||
| ##FORMAT=<ID=REPCN,Number=1,Type=String,Description="Number of repeat units spanned by the allele"> | ||
| ##FORMAT=<ID=SO,Number=1,Type=String,Description="Type of reads that support the allele; can be SPANNING, FLANKING, or INREPEAT meaning that the reads span, flank, or are fully contained in the repeat"> | ||
| ##ALT=<ID=STR16,Description="Allele comprised of 16 repeat units"> | ||
| ##ALT=<ID=STR18,Description="Allele comprised of 18 repeat units"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878_S1_HTT | ||
| chr4 3076603 . C <STR16>,<STR18> . PASS END=3076660;REF=19;RL=57;RU=CAG;VARID=HTT;REPID=HTT GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:16/18:16-16/18-18:4/7:319/320:0/0:34.624013 |
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|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| ##fileformat=VCFv4.3 | ||
| ##source=adVNTR ver. 1.3.3 | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of variant"> | ||
| ##INFO=<ID=VID,Number=1,Type=Integer,Description="VNTR ID"> | ||
| ##INFO=<ID=RU,Number=1,Type=String,Description="Repeat motif"> | ||
| ##INFO=<ID=RC,Number=1,Type=Integer,Description="Reference repeat unit count"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> | ||
| ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Spanning read count"> | ||
| ##FORMAT=<ID=FR,Number=1,Type=Integer,Description="Flanking read count"> | ||
| ##FORMAT=<ID=ML,Number=1,Type=Float,Description="Maximum likelihood"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CSTB_2_5_testdata.bam | ||
| chr21 45196323 . GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG GCGCGGGGCGGGGCGCGGGGCGGG,GCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGGGCGCGGGGCGGG . . END=45196359;VID=301645;RU=GCGCGGGGCGGG;RC=3 GT:DP:SR:FR:ML 1/2:60:39:21:0.863 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| ##fileformat=VCFv4.1 | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##command=GangSTR-2.4.2.12-9da7 --bam /scratch/bams/drive3/4512-JFI-0366_BXD196_phased_possorted_bam.bam --regions /scratch/regions/0705_mm10.bed --ref /scratch/ref/mm10.fa --str-info /scratch/strinfo/100519_mm10_strinfo_wo_stutt_recalc_many_samples.bed --chrom chr1 --trim-to-readlength 128 --drop-dupes --out result/4512-JFI-0366_BXD196/res_chr1 | ||
| ##contig=<ID=chr10,length=130694993> | ||
| ##contig=<ID=chr11,length=122082543> | ||
| ##contig=<ID=chr12,length=120129022> | ||
| ##contig=<ID=chr13,length=120421639> | ||
| ##contig=<ID=chr14,length=124902244> | ||
| ##contig=<ID=chr15,length=104043685> | ||
| ##contig=<ID=chr16,length=98207768> | ||
| ##contig=<ID=chr17,length=94987271> | ||
| ##contig=<ID=chr18,length=90702639> | ||
| ##contig=<ID=chr19,length=61431566> | ||
| ##contig=<ID=chr1,length=195471971> | ||
| ##contig=<ID=chr2,length=182113224> | ||
| ##contig=<ID=chr3,length=160039680> | ||
| ##contig=<ID=chr4,length=156508116> | ||
| ##contig=<ID=chr5,length=151834684> | ||
| ##contig=<ID=chr6,length=149736546> | ||
| ##contig=<ID=chr7,length=145441459> | ||
| ##contig=<ID=chr8,length=129401213> | ||
| ##contig=<ID=chr9,length=124595110> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of variant"> | ||
| ##INFO=<ID=RU,Number=1,Type=String,Description="Repeat motif"> | ||
| ##INFO=<ID=PERIOD,Number=1,Type=Integer,Description="Repeat period (length of motif)"> | ||
| ##INFO=<ID=REF,Number=1,Type=Float,Description="Reference copy number"> | ||
| ##INFO=<ID=GRID,Number=2,Type=Integer,Description="Range of optimization grid"> | ||
| ##INFO=<ID=EXPTHRESH,Number=1,Type=Integer,Description="Threshold for calling expansions"> | ||
| ##INFO=<ID=STUTTERUP,Number=1,Type=Float,Description="Stutter model - up prob"> | ||
| ##INFO=<ID=STUTTERDOWN,Number=1,Type=Float,Description="Stutter model - down prob"> | ||
| ##INFO=<ID=STUTTERP,Number=1,Type=Float,Description="Stutter model - p"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | ||
| ##FORMAT=<ID=REPCN,Number=2,Type=Integer,Description="Genotype given in number of copies of the repeat motif"> | ||
| ##FORMAT=<ID=REPCI,Number=1,Type=String,Description="Confidence intervals"> | ||
| ##FORMAT=<ID=RC,Number=1,Type=String,Description="Number of reads in each class (enclosing, spanning, FRR, bounding)"> | ||
| ##FORMAT=<ID=ENCLREADS,Number=1,Type=String,Description="Summary of reads in enclosing class. Keys are number of copies and values show number of reads with that many copies."> | ||
| ##FORMAT=<ID=FLNKREADS,Number=1,Type=String,Description="Summary of reads in flanking class. Keys are number of copies and values show number of reads with that many copies."> | ||
| ##FORMAT=<ID=ML,Number=1,Type=Float,Description="Maximum likelihood"> | ||
| ##FORMAT=<ID=INS,Number=2,Type=Float,Description="Insert size mean and stddev"> | ||
| ##FORMAT=<ID=STDERR,Number=2,Type=Float,Description="Bootstrap standard error of each allele"> | ||
| ##FORMAT=<ID=QEXP,Number=3,Type=Float,Description="Prob. of no expansion, 1 expanded allele, both expanded alleles"> | ||
| ##bcftools_filterVersion=1.6-49-ga2ffda9-dirty+htslib-1.7-1-gaf40c73 | ||
| ##bcftools_filterCommand=filter -r chr1:3000000-10000000 /storage/mikhail/100919_BXD_all_drive1_drive3_rep_stutt_model/result/4512-JFI-0366_BXD196/res_chr1.vcf.gz; Date=Sun Nov 24 18:06:49 2019 | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BXD196_0366 | ||
| chr1 3004986 . tctgtctgtctg . . PASS END=3004997;RU=tctg;PERIOD=4;REF=3;GRID=1,6;STUTTERUP=0.000632591;STUTTERDOWN=0.000632591;STUTTERP=0.953462;EXPTHRESH=3 GT:DP:REPCN:REPCI:RC:ENCLREADS:FLNKREADS:ML:INS:STDERR:QEXP 0/0:31:3,3:3-3,3-3:17,12,0,2:3,17:2,2:193.56:366.612,131.36:0,0:0,5.1188e-05,0.999949 |
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