Jordi D
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Activity overview
Latest activity by Jordi D-
Jordi D commented,
Dear all, I got some bam files from a collaborator and I would like to use the GATK workflow from the BaseRecalibrator tool. Its reference sequence had some control sequences like PhiX that I lacke...
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Jordi D commented,
Finally I got the mistake: since the SelectVariants was ran after a VQSR process, some variants were labeled with a FILTER field: VQSRTrancheSNP99.90to100.00 Then the parameter "exclude-filtered" s...
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Jordi D commented,
Hi all, Genevieve Brandt (she/her), just to summarize what I am looking for: Given the position #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 05-045 06-084 18-017 18-01...
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Jordi D commented,
Hi again Genevieve Brandt (she/her), First, I used the following code to filter the variants: gatk VariantFiltration \ -R ${refDir}/${assembly}/Homo_sapiens_assembly.fasta \ ...
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Jordi D commented,
Hi Genevieve Brandt (she/her), in fact I want to filter out any variant (phased or unphased) that doesn't meet the parameters. I am dealing with a multi-sample vcf (~80 samples) and I previously us...
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Jordi D commented,
Hi Genevieve Brandt (she/her). Thank you for the answer, I have carefully read the article. However, now I wonder if those variants with PID and PGT information, can be succesfully filtered with 'S...
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Jordi D created a post,
Haplotype Caller General Question
AnsweredDear all, I tried to perform a multisample variant calling using HaplotypeCaller(see command line below) To this end I used HaplotypeCaller over different samples and then combine them into a final...