Entering edit mode
5 months ago
Wasim
•
0
Hello I am a beginner in sequence alignment and Variant Calling. I am aligning the whole genome of bulls with Y chromosome reference seq. I have vcf that contains diploid and haploid but I wanna extract only haploid as I am interested in Y chromosom only. I am using this code to create vcf. bcftools mpileup -d 1000 -f Y.fasta -q 27 -Q 27 CMHR_3.bam | bcftools call -mv -Ov -o CMHR_2.vcf
can any one help me to get the exact vcf for Ychrom only please?
