Chr issue in BAM

[sybrohee]

Hi all,

When running vargrouper on a VCF file on hg38 with the corresponding BAM and FASTA, I ran into the following issue.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/celltics-_version_-py3.8.egg/celltics/tools/vargroup.py", line 667, in <module>
    cli()
  File "/usr/local/lib/python3.8/dist-packages/click-8.1.3-py3.8.egg/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/click-8.1.3-py3.8.egg/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.8/dist-packages/click-8.1.3-py3.8.egg/click/core.py", line 1635, in invoke
    rv = super().invoke(ctx)
  File "/usr/local/lib/python3.8/dist-packages/click-8.1.3-py3.8.egg/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.8/dist-packages/click-8.1.3-py3.8.egg/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/celltics-_version_-py3.8.egg/celltics/tools/vargroup.py", line 661, in cli
    main(input_file=input_file, output_file=output_file, bam_file=bam_file, merge_distance=merge_distance,
  File "/usr/local/lib/python3.8/dist-packages/celltics-_version_-py3.8.egg/celltics/tools/vargroup.py", line 628, in main
    records, var_dict = bam_and_merge_multiprocess(bam_file, vars_to_group, fq_threshold, min_reads,
  File "/usr/local/lib/python3.8/dist-packages/celltics-_version_-py3.8.egg/celltics/tools/vargroup.py", line 608, in bam_and_merge_multiprocess
    recs, var_dict_part = r.get().get_fat() if not debug and nthreads > 1 else r.get_fat()
  File "/usr/lib/python3.8/multiprocessing/pool.py", line 768, in get
    raise self._value
ValueError: invalid contig `chrchr11`

This seems to be due to the fact that vargrouper adds "chr" to the chromosome name when interrogating the BAM as it is supposed to work with a VCF file without chr and BAM that may potentially have one (function check_for_chr)

def check_for_chr(sam):
    """ Check sam file to see if 'chr' needs to be prepended to chromosome """
    if 'chr' in sam.references[0]:
        return True
    return False

It could be of interest to modify the function check_for_chr, so that it also takes the vcf file as an argument and checks that chr is used or not as prefix in the chromosome coordinates.

[sybrohee]

At the moment I solved the issue by making function check_for_chr always return False (if the fasta, bam and vcf have the same conting annotation it is OK).