只需要把两个4+8的值12作为过滤参数即可$ samtools view-b-F12a.bam>a.F12.bam#提取没有比对到参考序列上的比对结果$ samtools view-b-f4a.bam>a.f4.bam#提取bam文件比对到scaffold1上的比对结果,并保存成sam
I am using bcftools view -R regions.bed input.vcf.gz to extract only those variants present in regions.bed. However, I get only those variants not present in regions.bed, so exactly the opposite. I really don't know what is going on... Any help? Thanks! Anna I noticed something simi...
I try to use bcftools norm with the command : bcftools view --threads 6 \ -f .,PASS \ ${TMP_DIR}/${VCF} \ --regions-file ${interval} \ | \ bcftools norm \ -m - -w 10000 -f ${FASTA} --output-type z --output ${VCF_DIR}/${VCF/vcf.gz/select.vcf.gz} --threads 4 -...
/* vcfview.c -- VCF/BCF conversion, view, subset and filter VCF/BCF files.Copyright (C) 2013-2018 Genome Research Ltd.Author: Shane McCarthy <sm15@sanger.ac.uk> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation ...
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Then I can use bcftools view -S to explicitly remove samples by their ID, which I have identified manually as failing some thresholding criteria. This also is obviously cumbersome, and only works for FMT fields that are included in stats (e.g., not GQ or PL). I am not sure if I am...
I'm looking for triallelic records, for which the allele count of one of the alleles is zero. I'm doing bcftools view --min-alleles 3 --max-ac 0:minor $vcf, but that prints all records. For example this one: 20 61279 rs189899941 C A,T . PASS AR2=0.884;DR2=0.907;AF=0.009,...
run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y'); run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>''); @@ -1409,6 +1411,7 @@ sub test_vcf_norm my ($opts,%args...
If I use valgrind on a test I get this: @ seq3b[samtools.../bcftools]; valgrind bcftools query -f '%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' test/view.filter.vcf ==20105== Memcheck, a memory error detector ==20105== Copyright (C) 2002-2013, ...