Hello!
I obtained trio-based exome data (vcf files) from vendor. VCF files show PGT and PID for many rows. GATK explained them as Physical phasing...
6 results in 0.0028 seconds.
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Trio-based analysis: pipeline for phasing the data
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Incorrect Phasing using Beagle 4
Hello, I am using beagle 4 to phase several thousand samples (>500 trios) plus some single samples. When using the ibd=true, gt=vcfin.vcf, ped=pedin.ped... -
Haploid inspiration
Hi all
I'm looking for some inspiration/guidance on processing NGS data from haploid individuals. In a nutshell, we've sequenced at ~ 6X... -
Help: Beagle 4 phasing
Hello Everyone,
I am a newbie to BI and this is my first project so please bare with me. I was wondering if anyone has worked with Beagle... -
BEAGLE errors: Allele not in marker file / Number of fields in .gprobs isn't %3
I'm trying to phase a specific genome against the 1000 genomes data.
What I've done so far:- fastq-dump --split-3: SRA -> FastQ
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samtools Option to get genotype likelihood (GL)
I would like samtools mpileup to generate genotype likelihoods or what is described in the VCF FORMAT as GL. I can get PL which is fine (I know how to...
