linsson

very large pvalue qvalue difference

8

Hi all. I am running goatools v 0.6.10. The result for an enrichment analysis shows a very large pvalue-qvalue difference which sounds strange to me. Here is the command line:...

Dear developers, I am writing to you because it seems that bcftools stats does not take into account 2/2 type genotypes when calculating nNonRefHom in the counts per sample section....

snpgdsLDpruning result to gds/vcf

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Dear developer(s), I wonder if there is any chance to get a gds (or vcf) file once a snp dataset (with multiple samples inside) has been pruned. Unfortunately I am...

Build error

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I am trying to compile compute-runtime (I tried both 22.43.24595.30 and 22.43.24558 version) but I always reveive an error at "Generating ../../../../bin/built_ins/x64/spirv/fill_image3d.spv" Here is the complete log: -- The C...

vg giraffe hangs or stalls when reading large gzipped FASTQ files

22

**1. What were you trying to do?** I was trying to map paired-end reads from .fastp.fastq.gz files to a tomato pangenome graph using vg giraffe. Command structure (called inside a...

Again on vcf format

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Dear @singing-scientist, Thank you for developing and sharing SNPGenie. I would like to ask for some clarification regarding the appropriate input format, and I apologize if this has already been...

POS field apparently not corresponding to REF allele in vcf

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Hi, Thank you very much for sharing your tool. I am writing to you since I obtained a SV vcf file for a Tomato collection. While I was trying to...