Jordi D
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Recent activity by Jordi D Sort by recent activity-
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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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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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 18-0181...
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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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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 used...
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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 'Sel...