yeinhorn

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yeinhorn
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Israel
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  • Hi @Geraldine_VdAuwera, I usually get single exome each time from a different lab which uses a different sequencing machine and different coverage. I want to use VSQR in order to get good filtration, but since 1 exome isn't enough to build a reli…
  • i think plinkseq could do that, for example to set gentoypes with DP<=4 OR GQ<=20 as missing use : pseq INPUT.vcf write-vcf --mask geno.req=DP:ge:4,GQ:ge:20 > OUTPUT.vcf more details could be found here https://atgu.mgh.harvard.edu/plin…
  • Thanks @Sheila , Just to make sure: 1.Before making the recalibration step ("PrintReads"), indels don't have any quality score? 2.I think the default behavior of the PrintReads command is to NOT to keep the original qualities in order to save s…
  • Hi @Geraldine_VdAuwera, can you explain why the re-calibrated bam files are almost twice as big as the original bam file? e.g for input file realigned_reads.bam size of 4.1G, i get after the PrintReads command an output bam file " recal_reads.bam…
  • Hi @Geraldine_VdAuwera, 1.Can you explain me why do I need a large number of samples to use VSQR? aren't the samples independent? 2.does it matter if the samples are dependent (same family, same rare disease) or independent (random samples from r…
  • I think there's a typo. once finishing the 'Realign around Indels' step we have the 'realigned.bam' file, but then in the 'base recalibaration' step, the input file in the tutorial is 'realigned_20.bam' instead of ''realigned.bam' which results w…