I have VCF files (SNPs & indels) for WGS on 100 samples, but I want to only use a specific subset of 10 of the samples. Is there a relatively easy way About: Split VCF by sample, creating single-sample VCFs. Usage: bcftools +split [Options] Plugin options: -e, --exclude EXPR exclude sites for which the...Create a consensus sequence by applying VCF variants to a reference genome file bgzip All_samples.variants.withTags.vcf tabix -p vcf All_samples.variants.withTags.vcf.gz samtools faidx Ref_genome.fa chr1:1-1000 | bcftools consensus All_samples.variants.withTags.vcf.gz > chr1_1_1000.consensus.fa Original page. Calling SNPs from Short-Read Sequencing
On 2013Jun21, fixed a bug in table_annovar to have empty output when input is in five-column format, fixed a bug in table_annovar fo avsift output, fixed a bug when handling start position for multi-allelic SNPs in dbSNP, fixed a bug when scanning indels with multi-allelic variants in VCF DB file, fixed a bug when chr prefix is present in ... Randomly sample a subset of records from a VCF file, given a rate (vcfrandomsample). Select variants of a certain type (vcfsnps, vcfbiallelic, vcfindels, vcfcomplex, etc.) annotation. Annotate one VCF file with fields from the INFO column of another, based on position (vcfaddinfo, vcfintersect).
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