Hi,
anyone has an indea why I'm getting this error message?
In-----
samtools mpileup -gf ./Reference_Indexed/Human36.fa ./2007.0214 B.normal.merged.out.bam > normal.test.bcf
It generates sort of 3GB of data when the crash comes in.
Out----
mpileup] 1 samples in 1 input files
<mpileup> Set max per-sample depth to 8000
sh: line 24: 7723 Segmentation fault
It also does not parse the whole bam file when mpileup is piped into bcftools command as is suggested in the manual:
samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
BTW, pileup does not have any problems with the bam file. It has been generated by SAMTOOLS using SAM output of Stampy-BWA aligners.
Many thanks for any suggestions.
anyone has an indea why I'm getting this error message?
In-----
samtools mpileup -gf ./Reference_Indexed/Human36.fa ./2007.0214 B.normal.merged.out.bam > normal.test.bcf
It generates sort of 3GB of data when the crash comes in.
Out----
mpileup] 1 samples in 1 input files
<mpileup> Set max per-sample depth to 8000
sh: line 24: 7723 Segmentation fault
It also does not parse the whole bam file when mpileup is piped into bcftools command as is suggested in the manual:
samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
BTW, pileup does not have any problems with the bam file. It has been generated by SAMTOOLS using SAM output of Stampy-BWA aligners.
Many thanks for any suggestions.
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