samtools mpileup to get vcf files including GL information
hello,I use samtools mpileup to call individual snp and indel,my commond lines is samtools mpileup -ugf /ifshk4/PC_HUMAN_US/PROJECT/SZC10013-01_HUMassX/meijunpu/reference/hg18.fa UC5927.mapped.0.bam |../bcftools view -bvcg - |../bcftools view - |../vcfutils.pl varFilter -D 100 > UC5927.mapped.0.var.flt.vcf ,I got the vcf file,but I hope the vcf contains the GL(Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)) information,such as GT:GL 0/1:-323.03,-99.29,-802.53 ,which option I should to add ??? also,how to get GT(genotype),encoded as alleles values separated by “|”, not "/".anyone knows?please help me .
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM