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
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rayzghimire •
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.
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?
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.
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