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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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Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
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