bcftools Haploid variant calling
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9 weeks 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?

bcftools • 151 views
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