bcftools - creating indels

Question

[rayzghimire]

Hi, So I am converting fastq files into vcf. I wanted to know while calling variants how to include both SNPs and indels using samtools or bcftools.

Thank you

Answer 1

[Istvan Albert]

Your verbiage seems a bit all over.

You can't convert FASTQ to VCF - it is not a conversion problem.

Perhaps you mean to align FASTQ to a reference, create a BAM alignment file, then call SNPs from the BAM file with bcftools.

If so you don't need to specifically ask for indels, they would be produced along the way.

[rayzghimire]

Hi Albert, You are exactly right, that is what I wanted to do. Sorry should have been more clear. A little follow up on that- $ bcftools call --ploidy 1 -m -v -o results/bcf/SRR2584866_variants.vcf results/bcf/SRR2584866_raw.bcf I am using this command to call SNP is there another command in bcftools to call indels?

[Istvan Albert]

when we call a tool a SNP caller it almost always also calls insertions and deletions as well.

SNP calling is technically a misnomer. Most variation callers are SNV callers (bcftools included) and are able to produce all small nucleotide variations including insertions and deletions.