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Hi,
Using samtools 0.1.18 to produce an mpileup file from a single bam file, I find in the middle of one of the chromosomes that an extremely large sequence of "^@^@^@^@^@^@^@^@^@^@^@^@" is produced (several thousand characters long of this repeating). It overflows in both the forward and backward direction, as it disrupts the normal mpileup format in the lines immediately preceding and following.
Any idea what might cause this, and if there is a work-around?
This is from WES data at about 400x average depth coverage (mpileup file size is approx. 100Gb), so it is possible that for some base the read depth exceeded some maximum array size, causing buffer overflow - but just a guess.
Thanks!
Using samtools 0.1.18 to produce an mpileup file from a single bam file, I find in the middle of one of the chromosomes that an extremely large sequence of "^@^@^@^@^@^@^@^@^@^@^@^@" is produced (several thousand characters long of this repeating). It overflows in both the forward and backward direction, as it disrupts the normal mpileup format in the lines immediately preceding and following.
Any idea what might cause this, and if there is a work-around?
This is from WES data at about 400x average depth coverage (mpileup file size is approx. 100Gb), so it is possible that for some base the read depth exceeded some maximum array size, causing buffer overflow - but just a guess.
Thanks!