- Look at Dr. Zhang's files in directory:
/Users/kunzhang/WorkSpace/Exome/Solexa/NA12878
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
File:Zsnp qr.jpg
Other Parameters[edit]
- Types of SNPs: edit transition.pl
awk '{print $1 "\t" $2 "\t" $3 "\t" $4}' hiqual.no_dbSNP>hiqual.no_dbSNP.refcall
Scripts/transition.pl hiqual.no_dbSNP.refcall >hiqual.no_dbSNP.trans
- Results for high-quality SNPs:
'
|
transition
|
transversion
|
reference |
283 |
315
|
transition |
512 |
1
|
transversion |
|
852
|
|
File:Hiqual trans.jpg
'
|
transition
|
transversion
|
reference |
5319 |
9867
|
transition |
47545 |
10
|
transversion |
|
86105
|
|
File:Loqual trans.jpg
- There is a vast over-representation of homozygous SNPs of both types (transition-transition and transversion-transversion) and a slightly higher rate of single-transversion SNPs
- Plot quality and coverage of SNP types
paste loqual.no_dbSNP.refcall loqual.no_dbSNP.qr.txt >loqual.no_dbSNP.refqr
Scripts/transition.pl loqual.no_dbSNP.refqr >loqual.no_dbSNP.trans
grep '22$' loqual.no_dbSNP.trans|awk '{print $5"\t"$6}'>loqual.22.txt
File:Trans compare.jpg
- EDIT 8/4: Legend should have n=852 for 'Hi 22'
- Are the same trends observable for SNPs at dbSNP locations?
Error Characteristic[edit]
- Make heatmap for high-quality data set (title is wrong...)
File:Hiqual dbSNP.jpg
- What if we compare homozygous and heterozygous SNPs?
grep 'het' hiqual.in_dbSNP | awk '{print $6"\t"$8"\t1"}' >hiqual.in_dbSNP.het
mv hiqual.in_dbSNP.het hiqual.in_dbSNP.het.txt
grep 'het' hiqual.no_dbSNP | awk '{print $6"\t"$8"\t0"}' >hiqual.no_dbSNP.het.txt
File:Hiqual het dbSNP.jpg
- Similarly extract data for homozygous SNPs
File:Hiqual homo dbSNP.jpg