Ylaine/2009-8-3: Difference between revisions
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* Similar distributions of quality and coverage of non-dbSNP SNPs | * Similar distributions of quality and coverage of non-dbSNP SNPs | ||
[[Image:Zsnp_qr.jpg]] | [[Image:Zsnp_qr.jpg]] | ||
===Other Parameters=== | |||
* Types of SNPs: edit transition.pl |
Revision as of 17:58, 3 August 2009
- 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