rfuentes

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rfuentes
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  • @tommycarstensen A, sorry. It's not a real indel from a VCF file. I just made it for illustration. Most of the indel I see occur right after the first base: pos REF ALT 40 CCG C,CAACG --deletion and insertion after "C"(pos 4…
  • @tommycarstensen @Sheila I found this http://gatkforums.broadinstitute.org/discussion/5020/location-of-variant-in-multi-sample-calling#latest But does that mean the insertion/deletion can happen in any position relative to the ref string? For examp…
  • Thank you @tommycarstensen and @Geraldine_VdAuwera! I will inform my colleague about this. I'm not sure why they chose to use UG in the pipeline instead of HC. Do you think the VCF is unreliable because of these mixed cases or can you suggest any m…
  • Thank you, @Geraldine_VdAuwera!
  • Hi @Geraldine_VdAuwera I saw you answered a forum question which is almost the same as I posted above but I still don't fully understand the event indicated in each line. Why are they concatenated and not presented as 1 line per position if they ar…
  • @tommycarstensen & @Sheila I still don't understand why some positions(non variant) are concatenated in a single line while others are not. This is important for us because we are parsing multiple(3k) VCFs to generate a universe of variants. Th…
  • Hi Tommy, We included it to generate the consensus sequence of the whole genome. This project involves 3k rice genomes. I expect that EMIT_ALL_SITES will give each position as a separate line and not concatenated in a single REF. In my VCF, I found…
  • Hi Shiela, java -Xmx8g -jar /software/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /reference/japonica/reference.fa -I /output/filename.merged.bam -o filename.merged.vcf -glm BOTH -mbq 20 --genotyping_mode DISCOVERY -out_mode …