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...
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,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Descr...
$ 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...
##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##contig=<ID=1,length=249250621,assembly=b37> #CHROM POS ID REF ALT QUAL FILTER INFO I'd really rather use--regions-filebecause--targets-filecan miss these types of deletions, but it's hard because of the prob...
FILTER~"A" Both "A" and "A;B" pass FILTER!~"A" Neither "A" nor "A;B" pass Fix in commutative comparison operators, in some cases reversing sides would produce incorrect results (#1224; #1266) Better support for filtering on sample subsests Add SMPL_*/S* family of functions that...
{"strict-filter",no_argument,NULL,'s'}, {"no-version",no_argument,NULL,8}, {NULL,0,NULL,0} }; char *tmp; while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sN",loptions,NULL)) >= 0) { switch (c) { case 'N': args->do_indels = 0; br...
Those are two summary VCFs without genotypes (permitted by the spec). tr '|' '\t' << EOF | bgzip > C.vcf.gz ##fileformat=VCFv4.3 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Some metric"> #CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO chr1|123|.|A|C|.|.|AN=30 EOF tr '...
MARSseq.human.TTACGC.sam.sorted.bam MARSseq.human.GACCAG.sam.sorted.bam --annotate AD,DP,SP,INFO/AD | bcftools call -R gnomad.exomes.r2.0.2.sites.orig.chromadded.vcf.bgz -m -Ou | bcftools filter -Ou -i'DP>3 && QUAL>20' | bcftools sort -T tmp/ --max-mem 15G -Oz -o ...
// miscalculations through BAQ, STR analysis, etc. // So we put a cap on how good seqQ can be. // // Is it simply the equivalent of increasing -F filter? // Not quite, as the latter removes many real variants upfront. // This calls them and then post-adjusts quality, potenti...
{"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:"...