kokyriakidis

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kokyriakidis
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  • Hi! Could I have access to the custom lab process you work on to produce the right data? I want to work on liquid biopsy but I am struggling to find a good protocol
  • Hi @shlee Patches do not change the chromosomal coordinates right? They only add information. GRCh38.p12 has the latest and most accurate information right? This is the case for dbSNP151 too. So, wouldn't be the best to do all my research with the …
  • Hi @bhanuGandham Yes but the patch versions of GRCh38 have the same chromosomal coordinates. They only add on information. So all the resource file in the bundle should be aligned equally(?) In best practices it states that we should use dbSNP >…
  • Hi @bhanuGandham , So, when you say that I need to create all the reference resources, you mean that I have to create my own files for the VQSR step (for training, truth etc)? Can't I use the same files for RBQS and VQSR from the bundle and just ch…
  • Hi @slee , 1) Can someone use the latest patch GRCh38.p12 instead of the reference file in the bundle? 2) dbSNP151 vcf file is based on GRCh38.p7 reference. Should I use this particular patch or can I use GRCh38.p12? 3) If I use a newer reference f…
  • Hi, 1) dbSNP151 file states that it uses as reference the GRCh38.p7. When I use dbSNP151 in GATK4 should I use this specific reference build or I can use whatever build I want, etc GRCh38.p12 (latest)? 2) Can I use whatever build of GRCh38.p* I w…