Dear all, I would like to use samtools to call SNP. I use the latest version 1.0. First, I have to generate bcf file. I run the following command.
samtools mpileup -t DP -ugf my.fasta my.bam the result is always like this: [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 Aborted If I just run samtools mpileup -f my.fasta my.bam it works fine. I have no idea what happens. If I go back to use samtools-0.1.19 to run samtools mpileup -uD -f my.fasta my.bam everything is okay. Could anyone helps me? Thank you.I also parsed the BAM file to short one. I found when the line comes to 88, it will aborted. Before line 88, everythin is fine. But I checked the file, I didn't see anything wrong. Please refer the attachment.
Sung-Huan
short.bam
Description: GNU Zip compressed data
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