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>
