$ bcftools filter -i ' FILTER=="PASS" && DP>20 && GQ>100 && QUAL>100' "$outDIR"_norm/"$out_basen (3) 提取 突变位点的AD和DP,顺便可以计算 VAF: $ bcftools query-f'[%AD]\n'"$outDIR"/"$out_basename"|awk'BEGIN{FS=","}{ print $2 }'>>"$outDIR"_tmp/"$out_basename"_AD...
gatk MergeVcfs -I concat-a.vcf -I concat-b.vcf -O combine_a_b_diffsample_allsites_gatk.vcf 两个命令执行结果完全一致,结果如下。 ##fileformat=VCFv4.2##FILTER=<ID=q10,Description="Quality below 10">##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">##FORMAT=<ID=GQ,Numb...
bcftools filter New--mask,--mask-fileand--mask-overlapoptions to soft filter variants in regions (#1635) bcftools +fixref The-m idoption now works also for non-dbSNP ids, i.e. not justrsINT New-m flip-allmode for flipping all sites, including ambiguous A/T and C/G sites ...
By looking at all files, there are instances of not checking the return of hts_readlist() in bin.c, filter.c, mpileup.c, vcfconvert.c (4 instances), vcffilter.c, vcfquery.c, plugins/color-chrs.c (2 instances), plugins/contrast.c, plugins/fill-tags.c, plugins/GTsubset.c, plugins...
gatk MergeVcfs -I concat-a.vcf -I concat-b.vcf -O combine_a_b_diffsample_allsites_gatk.vcf 两个命令执行结果完全一致,结果如下。 ##fileformat=VCFv4.2##FILTER=<ID=q10,Description="Quality below 10">##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">##FORMAT=<ID=GQ,Numb...
char *filter_str; int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE const uint8_t *smpl_pass; int set_gts; char *soft_filter; // drop failed sites or annotate FILTER column?int...
filter_t *filter; char *filter_str; int filter_logic; // one of FLT_INCLUDE/FLT_EXCLUDE (-i or -e) bcf_srs_t *files; bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header char **argv, *format, *sample_names, *subset_fname, *targets_...
$ cat out.vcf ##fileformat=VCFv4.3 ##FILTER=<ID=PASS,Description="All filters passed"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##contig=<ID=chr20> ##reference=hg38 ##INFO=<ID=FOO,Number=1,Type=String,Description="Yet another header line"> ##bcftools_annotate...
#CHROM POS ID REF ALT QUAL FILTER INFO 7 897 . GGAATTAAGA G . . . 7 910 . G C . . . 3 changes: 3 additions & 0 deletions 3 test/test.pl Original file line numberDiff line numberDiff line change @@ -286,6 +286,8 @@ run_test(\&test_vcf_norm,$opts,in=>'norm.phased-...
{"strict-filter",no_argument,NULL,'s'}, {"no-version",no_argument,NULL,8}, {"write-index",optional_argument,NULL,14}, {"write-index",optional_argument,NULL,'W'}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sNag:"...