Hello everyone, I used bctools mpileup and bcftools call on my bam file and I used VCFfilter tool to filter for QUAL and it worked. Now I want to filter for RPBZ in a range between -5 and +5. I tried to set the filtering value like this RPBZ > -5 & RPBZ < 5 but I got an error. I also tried to se…

UPDATED usage help for negative values when using VCFFILTER [image] VCFfilter: can´t eliminate negative values For context, please see this two line discussion from the vcffilter tool author: vcffilter core dumped on negative values · Issue #249 · vcflib/vcflib · GitHub That means the query you…

Welcome, @giuliag89 [image] giuliag89: Could the problem be the minus simbol? Yes, probably. Would you please copy/paste back a line from the VCF file that contains an example value you want to remove that is a negative value? Or even better, would you share the file itself in a history alo…

Hi Jennaj, this is the link of the history with the failed query runs: url: https://usegalaxy.eu/u/giuliag89/h/run-sample-2-error Thanks

Hi @giuliag89 The history isn’t shared anymore, or wasn’t fully shared originally. You can just post back a few lines of the data. I’m more curious about how those are structured in the VCF text itself, but I guess you can also share the history if it shows how/where those values were introduced (…

Hi, I made the history shared again if you want have a look: url: https://usegalaxy.eu/u/giuliag89/h/run-sample-2-error Here few lines of the vcf file: chr13 32906574 . T A 3.38992 . DP=3107;ADF=4,1516;ADR=1399,4;AD=1403,1520;DPR=1403,1520;VDB=0;SGB=-0.693147;RPBZ=-47.9879;MQBZ=0;MQSBZ=0;BQBZ=-47…

Hi @giuliag89 Great, thanks for sharing. The tool seems to be working correctly, and negative values are accepted. Try removing the space between the - and 5. So this: TERM > -5 instead of TERM > - 5 The two filters might need to be in separate filter blocks. I didn’t get any data passing throu…

Negative values with VCF filter tool

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jennaj May 13, 2024, 6:58pm 7

UPDATED usage help for negative values when using VCFFILTER

An alternative tool is SNPSIFT FILTER