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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 [[Image:Zsnp_qr.jpg]] ===Other Parameters=== * Types of SNPs: edit transition.pl awk '{print $1 "\t" $2 "\t" $3 "\t" $4}' hiqual.no_dbSNP>hiqual.no_dbSNP.refcall Scripts/transition.pl hiqual.no_dbSNP.refcall >hiqual.no_dbSNP.trans * Results for high-quality SNPs: {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''transition''' | align="center" style="background:#f0f0f0;"|'''transversion''' |- | reference||283||315 |- | transition||512||1 |- | transversion||||852 |- | |} [[Image:Hiqual_trans.jpg]] * Low-quality SNPs: {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''transition''' | align="center" style="background:#f0f0f0;"|'''transversion''' |- | reference||5319||9867 |- | transition||47545||10 |- | transversion||||86105 |- | |} [[Image:Loqual_trans.jpg ]] * There is a vast over-representation of homozygous SNPs of both types (transition-transition and transversion-transversion) and a slightly higher rate of single-transversion SNPs * Plot quality and coverage of SNP types paste loqual.no_dbSNP.refcall loqual.no_dbSNP.qr.txt >loqual.no_dbSNP.refqr Scripts/transition.pl loqual.no_dbSNP.refqr >loqual.no_dbSNP.trans grep '22$' loqual.no_dbSNP.trans|awk '{print $5"\t"$6}'>loqual.22.txt [[Image: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=== * Make heatmap for high-quality data set (title is wrong...) [[Image: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 [[Image:Hiqual_het_dbSNP.jpg]] * Similarly extract data for homozygous SNPs [[Image:Hiqual_homo_dbSNP.jpg]]
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