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freebayes -f /share/home/shh/download/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa -iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 6 ${souporcell_out}minitagged_sorted.bam
##fileformat=VCFv4.1
#…
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compilation output:
g++ -DHAVE_CONFIG_H -I. -DUNIX -I/share/disk6-2/leihx/sunjy/software/boost-1.45.0/include -DHAVE__BOOL -D__NOPLUGIN__ -fopenmp -O3 -MT encore.o -MD -MP -MF .deps/encore.Tpo …
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Hi,
Recently, I have get the access to dataset EGAD00001007718 from EGA, however all the data are cram format. If I want to covert the data to bam format, the reference genome is necessary for…
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Expected Behavior
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For Bugs:
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### Environment
#### Steps to Reproduce
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**1. What were you trying to do?**
Hi VG Team. I am trying to genotype a VCF using the workflow as described here:
https://github.com/vgteam/vg/wiki/SV-Genotyping-and-variant-calling.
Specific…
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Hi, recently i use the Delly(Version: 1.1.6) to call sv for tumor-only sample , and i meet some problem:
the delly command is:
delly call -t ALL -g hg19.fasta -x human.hg19.excl.tsv -q 20 -s 15 -a 5…
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Hello,
First, I want to express my gratitude for developing xTEA.
I am encountering an issue while using xTEA’s case-control mode to identify somatic transposon (specifically Alu) insertions. Ba…
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Hi,
I am currently utilizing `Manta` for structural variant calling and subsequently processing the results with `Bcftools merge` and `Truvari collapse` to generate a project-level VCF (pVCF). Duri…
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Thanks a lot for your hardworking on PING. I was trying to use my WES and WGS data to do KIR genotyping, but it returned with partial results. manualCopyNumberFrame.csv and finalAlleleCalls.csv are no…
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Hi Ryan,
I have a new question about processing multiple samples by LUMPY... I 've 808 wgs samples at 30X (human and ref genome which I used is hs37d5 like 1000G). I generate the discordant and sp…