Commits for angie
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v291_preview2 to v291_base (2013-10-14 to 2013-10-21) v291
- 1. Rebuilding ucscAlleleFreq (and hence snp138) because when updatingthe allele frequencies in August, I forgot to use the new -deDupTGP
command line arg.
2. As b0b suggested, I'm including variants in snp138Common if they
are 100% non-reference. Technically their MAF is 0 -- but differing
from the reference sure is common! And those wishing to filter out
common variants would want to filter those out.
refs #11438
- src/hg/makeDb/doc/hg19.txt - lines changed 46, context: html, text, full: html, text
- src/hg/utils/automation/categorizeSnps.pl - lines changed 82, context: html, text, full: html, text
- src/hg/utils/automation/doDbSnp.pl - lines changed 2, context: html, text, full: html, text
- Heroic ML #11775 users provoked yet another bug: an insertion at theCDS/UTR boundary was falling through the cracks and nothing was output
for it. It should be classified as UTR.
refs #11775
- Another fix for ML #11775: use a real alternate allele for intergenicvariants, so users aren't misled by the VEP placeholder "-".
- src/hg/lib/annoGratorGpVar.c - lines changed 33, context: html, text, full: html, text
- revCompSnp's reversing of the sorted reverse-complemented alleleswas enough to maintain sorting of [ACGT] alleles, but not when '-'
is in the mix. When merging lists that weren't correctly sorted,
we ended up with two entries for '-' in the combined output.
Now we're outright sorting them so that won't happen again.
refs #11943, #11954
- src/hg/utils/automation/snpAddTGPAlleleFreq.pl - lines changed 1, context: html, text, full: html, text
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