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Revision as of 02:21, 17 June 2014
, 02:21, 17 June 2014→Did I find interesting variants?
Did you see a variant at the position?
Did you see a variant at the position?
$GC/bin/tabix $OUT/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 | head -1
22 36661906 . A G 18 PASS DP=409;MQ=59;NS=62;AN=124;AC=2;AF=0.013827;AB=0.4065;AZ=-0.5287;
FIC=-0.0092;SLRT=-0.0075;HWEAF=0.0138;HWDAF=0.0276,0.0000;LBS=36,36,0,0,1,1,0,0;
OBS=145,191,0,0,3,2,0,0;STR=-0.040;STZ=-0.740;CBR=0.008;CBZ=0.144;IOR=0.000;IOZ=-1.370;
AOI=-5.614;AOZ=-4.243;LQR=0.178;MQ0=0.000;MQ10=0.000;MQ20=0.000;MQ30=0.000;SVM=1.51214
GT:DP:GQ:PL 0/0:4:28:0,12,65
Let's check the sequence data to confirm that the variant really exists
$GC/bin/samtools tview $IN/bams/HG01242.recal.bam $REF/human.g1k.v37.chr22.fa
* Type 'g' to go to a specific position
* Type 22:36661906 to move to the position
* Press arrows to move between positions
* Press 'b' if you want to color by base quality
* Press '?' for more help
[[File:Samtoolstviewsnp.png]]
