I use
> bwa-0.7.15/bwa mem -t 16 genome_seq/index.fa \
forwardseq.fq reverseseq.fq > mapped.sam
then
> samtools view -bhS mapped.sam | samtools sort - mapped.sam.sorted
(to prepare data for variant calls) when I see this error on all 4 sets of
our sequences (i.e. reproducible):
[bam_header_read] EOF marker is absent. The input is probably truncated
when I searched for clues I found it was discussed on older version of bwa
prior to 2013 (it seems there were patches to solve the unexpected
problem). I wonder is this something new or the fixes were not implemented
in new bwa versions? How to find out if the results are good for
subsequence varant calling?
Thanks in advance!
Zhiliang
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