Ylaine/2009-8-3: Difference between revisions

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* Types of SNPs: edit transition.pl
* Types of SNPs: edit transition.pl
  awk '{print $1 "\t" $2 "\t" $3 "\t" $4}' hiqual.no_dbSNP>hiqual.no_dbSNP.refcall
  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:
{| {{table}}
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''transition'''
| align="center" style="background:#f0f0f0;"|'''transversion'''
|-
| reference||283||315
|-
| transition||512||1
|-
| transversion||||852
|-
|
|}
[[Image:Hiqual_trans.jpg]]

Revision as of 19:48, 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

File:Zsnp qr.jpg

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

File:Hiqual trans.jpg