Question: direct call of indels/snps with bcftools?
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gravatar for cristina_sabiers
2.5 years ago by
Spain
cristina_sabiers40 wrote:

I am wondering...

With vcftools I can call directly my snps and indels from my vcf file, but with bcftools I only found this way where I need the bam file, cant I use a code where I take out my snps and indels directly with bcftools from my vcf file?

Thanks

1) To call only SNPs:

samtools mpileup --skip-indels -d 250 -m 1 -E --BCF --output-tags DP,DV,DP4,SP -f <reference genome.fa=""> -o <output.bcf> <list of="" input="" bam="" files="">

bcftools index <output.bcf> <indexed.bcf>

bcftools call --skip-variants indels --multiallelic-caller --variants-only -O v <output.bcf> -o <output.vcf>

2) To call only Indels:

samtools mpileup -d 250 -m 1 -E --BCF --output-tags DP,DV,DP4,SP -f <reference genome.fa=""> -o <output.bcf> <list of="" input="" bam="" files="">

bcftools index <output.bcf> <indexed.bcf>

bcftools call --skip-variants snps --multiallelic-caller --variants-only -O v <output.bcf> -o <output.vcf>

3) To call both SNPs and indels:

samtools mpileup -d 250 -m 1 -E --BCF --output-tags DP,DV,DP4,SP -f <reference genome.fa=""> -o <output.bcf> <list of="" input="" bam="" files="">

bcftools index <output.bcf> <indexed.bcf>

bcftools call --multiallelic-caller --variants-only -O v <output.bcf> -o <output.vcf>

snp bcftools • 957 views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.5 years ago by cristina_sabiers40
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