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Questions - gatk

GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

I can't seem to get GATK to recognise the number of available threads. I am running GATK (4.2.4.1) in a conda environment which is part of a nextflow (v20.10.0) pipeline I'm writing. For whatever reas...
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dthorbur

java

multithreading

gatk

Votes: 0

Answers: 2

Latest Answer

In case anyone else has the same problem, it turned out I had to configure the submission as an MPI job. So on the HPC I use, here is the nextflow process: process DNA_HCG { errorStrategy { sleep(Ma...
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dthorbur

Snakemake integrate the multiple command lines in a rule

The output of my first command line "bcftools query -l {input.invcf} | head -n 1" prints the name of the first individual of vcf file (i.e. IND1). I want to use that output in selectvariants...
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user3224522

python

bash

shell

snakemake

gatk

Votes: 0

Answers: 3

Latest Answer

There are several options, but the easiest one is to store the results into a temporary bash variable: rule selectvar: ... shell: """ myparam=$(bcftools query -l {...
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SultanOrazbayev

Snakemake first genotype of a vcf file as wildcard in output

In the second rule I would like to select from the vcf file containing bob, clara and tim, only the first genotype of dictionary (i.e. bob) in roder to get as output in the second rule bob.dn.vcf. Is ...
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user3224522

python

snakemake

gatk

Votes: 0

Answers: 1

Latest Answer

There are at least two options: explicitly specify output: rule somerulename: output: out="FAM1/bob.dn.vcf" impose constraints on wildcard values: rule somerulename: out...
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SultanOrazbayev

How to run ensembl-vep in conda

I’ve installed like so: conda install ensembl-vep=105.0-0 And then installed the human cache like this: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdf...
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Mike

variant

vcf-variant-call-format

vcftools

gatk

Votes: 0

Answers: 1

Latest Answer

I found the answer. You need to add both --cache and --dir_cache arguments: vep --cache --dir_cache "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-105....
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Mike

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