Hi,
I'm new to the forum and I'm not sure if this has been covered before but I am currently trying to do samtools mpileup on multiple bam files.
When I do variant callling on the whole genome it works fine. The problem is when using the - r to only call variants within a certain part of the genome I get the following message:
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
I have indexed the bam files so that there is a .bam file and .bam.bai file for each sample in the same folder I am working from with the same prefix.
I guess this is something to do with the indexing not working but I can't seem to find a specific answer when relating to mpileup -r.
Thanks in advance. Let me know if you need any other info.
Ben
I'm new to the forum and I'm not sure if this has been covered before but I am currently trying to do samtools mpileup on multiple bam files.
When I do variant callling on the whole genome it works fine. The problem is when using the - r to only call variants within a certain part of the genome I get the following message:
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
I have indexed the bam files so that there is a .bam file and .bam.bai file for each sample in the same folder I am working from with the same prefix.
I guess this is something to do with the indexing not working but I can't seem to find a specific answer when relating to mpileup -r.
Thanks in advance. Let me know if you need any other info.
Ben