Ylaine/2009-8-3: Difference between revisions
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Scripts/transition.pl loqual.no_dbSNP.refqr >loqual.no_dbSNP.trans | Scripts/transition.pl loqual.no_dbSNP.refqr >loqual.no_dbSNP.trans | ||
grep '22$' loqual.no_dbSNP.trans|awk '{print $5"\t"$6}'>loqual.22.txt | grep '22$' loqual.no_dbSNP.trans|awk '{print $5"\t"$6}'>loqual.22.txt | ||
[[Image:Trans_compare.jpg]] |
Revision as of 22:48, 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
awk '{print $1 "\t" $2 "\t" $3 "\t" $4}' hiqual.no_dbSNP>hiqual.no_dbSNP.refcall Scripts/transition.pl hiqual.no_dbSNP.refcall >hiqual.no_dbSNP.trans
- Results for high-quality SNPs:
' | transition | transversion |
reference | 283 | 315 |
transition | 512 | 1 |
transversion | 852 | |
- Low-quality SNPs:
' | transition | transversion |
reference | 5319 | 9867 |
transition | 47545 | 10 |
transversion | 86105 | |
- There is a vast over-representation of homozygous SNPs of both types (transition-transition and transversion-transversion) and a slightly higher rate of single-transversion SNPs
- Plot quality and coverage of SNP types
paste loqual.no_dbSNP.refcall loqual.no_dbSNP.qr.txt >loqual.no_dbSNP.refqr Scripts/transition.pl loqual.no_dbSNP.refqr >loqual.no_dbSNP.trans grep '22$' loqual.no_dbSNP.trans|awk '{print $5"\t"$6}'>loqual.22.txt