I have three sequencing libraries of single individual mapped to a reference using
bwa-mem. I would like to merge the three unsorted
.sam files I have so, I can call variants and heterozygosity estimates using atlas. Atlas requires one input mapping file (
bam) with defined read groups because it estimates the error profiles of different libraries separately.
How can I merge multiple sam files? Preferably avoiding java (Picard tools).
I tried to figure out a solution using
samtools 1.3. I sorted individual files using
samtools sort, then I used
samtools merge -r merged.bam s1.sort.sam s2.sort.sam s3.sort.sam to merge the sorted files. However, the read group didn't make it to the header (and the variant caller I use is complaining about it), also the read group is stupidly the file name.
I tried to define meaningful readgroup names using procedure described on BioStars, but I found that this will just change the header, it does not adjust the names of read groups defined by
samtools merge (the file names).
Following this related thread on SeqAnswers, I tried to define the correct header with read groups corresponding to merged file names:
samtools -rh rg.txt merged.bam s1.sort.sam s2.sort.sam s3.sort.sam
rg.txt is a file with header
output of samtools view -H s1.sort
However, the header still had not the read group, I guess because sam header accepts only tagged items to be specified (something like
@RG XY:s1.sort). So, I looked into the merged
bam and I found that the tag of RG is
Z:. So I tried to just rename header of the merged file using
samtools reheader, but then samtools complain about the fact that a tag needs to be of length 2:
Malformed key:value pair at line 123: "@RG Z:s1.sort"
Segmentation fault (core dumped)
I have opened an issue to report this strange incompatibility of read groups generated by
samtools merge with
I would like solution to :
- create a bit more standardized read group names (
- avoid pointless writing to disk like in sam -> sorted.sam -> merged.bam case (can be probably achieved through "pipes and tees", thanks @bli)
I also know that I can specify RG to bwa, so the sam files will have read groups defined in the first place. But I do not like the idea of remapping three libraries just to create correct formatting of read groups.