direct call of indels/snps with bcftools?
0
0
Entering edit mode
6.3 years ago

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 • 2.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 2462 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6