I have observed seemingly unstable outputs from the mpileup using default settings (identical to those suggested in the bowtie and samtools tutorials) and seek suggestions on how to resolve the issue. A few lines of the problematic output below. Note that allele frequencies (AF1, AFE) are nonzero, but readcounts (DP4; and other columns) are missing information. am running samtools from a 32Gb RAM system with 12x2.67Gb cores using CentOS5.5, and I am reference mapping a few million reads against a genome of approx 400Mb with >2k scaffolds for a few samples. Has anyone observed this, too, and if so, what solutions would there be to generate complete, healthy output?
thanx a lot in advance!!
scaffold_8 18567961 . C T 21.8 . AF1=1.000;AFE=0.689;DP4=0,0,0,0;MQ=0
scaffold_8 18579230 . C A 36.2 . AF1=0.500;AFE=0.499;DP4=0,0,0,0;MQ=0
scaffold_9 246255 . A T 4.77 . AF1=0.997;AFE=0.417;DP4=0,0,0,0;MQ=0
scaffold_9 246263 . A G 4.77 . AF1=0.997;AFE=0.417;DP4=0,0,0,0;MQ=0
scaffold_9 338143 . A G 99 . AF1=1.000;AFE=1.000;DP4=0,0,0,0;MQ=0
scaffold_9 338163 . A G 43.8 . AF1=1.000;AFE=0.694;DP4=0,0,0,0;MQ=0
scaffold_9 744547 . C G 99 . AF1=1.000;AFE=0.997;DP4=0,0,0,0;MQ=0
scaffold_9 753409 . C G 99 . AF1=1.000;AFE=1.000;DP4=0,0,0,0;MQ=0
scaffold_9 793195 . A G 61 . AF1=1.000;AFE=0.833;DP4=0,0,0,0;MQ=0
thanx a lot in advance!!
scaffold_8 18567961 . C T 21.8 . AF1=1.000;AFE=0.689;DP4=0,0,0,0;MQ=0
scaffold_8 18579230 . C A 36.2 . AF1=0.500;AFE=0.499;DP4=0,0,0,0;MQ=0
scaffold_9 246255 . A T 4.77 . AF1=0.997;AFE=0.417;DP4=0,0,0,0;MQ=0
scaffold_9 246263 . A G 4.77 . AF1=0.997;AFE=0.417;DP4=0,0,0,0;MQ=0
scaffold_9 338143 . A G 99 . AF1=1.000;AFE=1.000;DP4=0,0,0,0;MQ=0
scaffold_9 338163 . A G 43.8 . AF1=1.000;AFE=0.694;DP4=0,0,0,0;MQ=0
scaffold_9 744547 . C G 99 . AF1=1.000;AFE=0.997;DP4=0,0,0,0;MQ=0
scaffold_9 753409 . C G 99 . AF1=1.000;AFE=1.000;DP4=0,0,0,0;MQ=0
scaffold_9 793195 . A G 61 . AF1=1.000;AFE=0.833;DP4=0,0,0,0;MQ=0
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