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I've checked this specific position with IGV and out of ~47 reads that align in this position 3 of them are A, the rest are C. The A change is happening at the beginning of the reads. The rest of the bases are ok, so there is no change of a C to th…
The IGV does shows the presence of the alternative allele. Must I assume that the AF output is rounded out? The other problem I see is that when checking the AD, some of the paramters are also 0, so I cant calculate manually this either.
Understood, so I should add ReassignOneMappingQuality -RMQF 255 -RMQT 60 to the previous command, right? I was looking in this documentation and no reference to MapQ is done. https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_ga…
Just another question related to this. I'm following GATK's best practices protocol for RNAseq. And there is one step that confuses me. Split'N'Trim + ReassignMappingQuality I have done java -Xmx20g -jar /home/Programas/GATK/GenomeAnalysisTK.jar …
Yes I meant that protocol. It's giving me painful times. i just wanted to try it among other three which includes GATK's best practices. In the meantime. Can I use the ouput of theses commands for any other RNAseq variant calling program besides th…