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==Resolved the Majority of SNV Calling Error== * These are the ones that are low confidence in Chamber 18 (AlleleCountCh15HLA0mismatchCh18complement.txt). The high quality ones were removed from list. The criteria of confidence here was ALT base frequency > REF base. It is much better than previously removing low quality base, which both chamber were called the same ALT. Some issue like the pattern misalignment up there were only masked but not removed. $ perl /home/ericchu/softwares/countbase.pl PileupCh15HLA0mismatchCh18complement.txt AlleleCountCh15HLA0mismatchCh18complement.txt $ more AlleleCountCh15HLA0mismatchCh18complement.txt chr6 31240473 T C Depth = 3 A0, C2, G0, T1 chr6 31240489 A G Depth = 3 A1, C0, G2, T0 chr6 31240759 A G Depth = 4 A1, C0, G3, T0 chr6 31240854 C A Depth = 3 A2, C1, G0, T0 chr6 31240864 C T Depth = 3 A0, C1, G0, T2 $ perl /home/ericchu/softwares/countbase.pl PileupCh18HLA0mismatchCh15complement.txt AlleleCountCh18HLA0mismatchCh15complement.txt $ more AlleleCountCh18HLA0mismatchCh15complement.txt chr6 31134118 C A Depth = 91 A66, C-107, G132, T0 $ wc -l AlleleCountCh18HLA0mismatchCh15complement.txt 1 AlleleCountCh18HLA0mismatchCh15complement.txt $ grep 31134118 PileupCh18HLA0mismatchCh15complement.txt chr6 31134118 C 91 ..$,,,,$,.....$.,,,.+3GAG.+3GAG.+3GAG.+3GAG.+3GAG,+3gag,.+3GAG.+3GAG,+3gag,+3gag,$.$,+3gag.$.+3GAG.+3GAG..+3GAG,+3gag.+3GAG,+3gag,+3gag,+3gag,+3gag.+3GAG.+3GAG.+3GAG,+3gag.+3GAG.+3GAG.+3GAG,+3gag.+3AAG.+3GAG,+3gag.+3GAG.+3GAG.+3GAG.,+3gag,+3gag,+3gag,+3gag,+3gag,+3gag,+3gag.+3GAG.+3GAG.+3GAG.+3GAG,+3gag.+3GAG.+3GAG,+3gag,+3gag,+3gag,+3gag,+3gag.+3GAG.+3GAG,+3gag,+3gag.+3GAG.+3GAG.+3GAG,+3gag,+3gag,+3gag.+3GAG..+3GAG^]G^]G^]g BB<BB0FFFFFBFFFBFFBBFFFFFFIFFIFBBBBBFIIIIIIFIBFFIFIFFFIfFFFFBFeFIFIFFIFBB'FFI7BIIIF0BBBFBB<
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