Ylaine/2009-8-3
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- Look at Dr. Zhang's files in directory:
/Users/kunzhang/WorkSpace/Exome/Solexa/NA12878
- Copy best quality one:
cp NA12878_061009_061109_40bp_sequence.qualTrimmed.soapsnp.pileup.variants.txt ~/NA12878/hiqual
- Separate into hits and misses:
grep 'rs' hiqual>hiqual.in_dbSNP grep -v 'rs' hiqual>hiqual.no_dbSNP
- 1963/13394 not in dbSNP (14.7%)
- Get low-quality SNPs:
cp NA12878_072109_lib_sequence.qualTrimmed.soapsnp.pileup.variants.txt ~/NA12878/loqual
- 148846/169073 not in dbSNP (88.0%)
- Similar distributions of quality and coverage of non-dbSNP SNPs
Other Parameters
- Types of SNPs: edit transition.pl
awk '{print $1 "\t" $2 "\t" $3 "\t" $4}' hiqual.no_dbSNP>hiqual.no_dbSNP.refcall