Chloé Girard
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Activity overview
Latest activity by Chloé Girard-
Chloé Girard commented,
Dear all,Sorry I didn't update sooner, the project got sidetracked @gouret 's solution worked (removing the space) for all --filter-expressionSo the code now reads thus: gatk VariantFiltration \-R ...
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Chloé Girard commented,
Dear Bhanu, Thank you for your message The exact command line that you used when you had the problem (in a text file). #!/bin/bash#PBS -N Nselectvariants#PBS -q lowprio#PBS -j oe#PBS -l select=1:...
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Chloé Girard commented,
Hello Banhu, Thanks for your reply.My code now reads: gatk VariantFiltration \-R ~/Genomes/TAIR10_chr_all.fasta \-V ~/$sample1.vcf.gz \-O ~/$sample1$addon.vcf.gz \--filter-name "QD2" \--filter-expr...
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Chloé Girard created a post,
VariantFiltration MQRankSum error: "-12.5 is not a recognized option"
AnsweredDear all, I'm using GATK version 4.1.9.0 I am trying to filter variants from a VCF files generated through HaplotypeCaller (output: gvcf) and then GenotypeGVCF (output: vcf), using GATK v4.1.9.0...