[mira_talk] Parse error at line 84: unmatched CIGAR operation
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 27 Mar 2013 15:18:24 -0400
Good afternoon,
I need to do some samtools mpileups and I have been trying to generate BAM
files from mira's output without success.
The data are from mapping assemblies using various versions of the 3.9.x series
of mira.
A. If I use convert_project to generate a sam file from a maf file, all goes
well, and I can view the assembly in Tablet. However, either doing:
$ samtools view -bS STRAIN.sam > STRAIN.bam
or, after generating an index from the STRAIN_unpadded.fasta file using
samtools faidx:
$ samtools view -bt STRAIN_unpadded.fasta.fai STRAIN.sam > STRAIN.bam
generates a Parse error at line 84: unmatched CIGAR operation
B. Peter Cock's maf2sam.py (version 2.0) hangs when I try to convert the maf
file to a sam file.
C. Before I had heard of maf2sam.py or before convert_project's ability to
generate sam files, I used to make sam files by filtering caf files through
gap5, i.e.
$ tg_index-o STRAIN_gap5db STRAIN.caf
$ gap5_export -format sam -out STRAIN.sam STRAIN_gap5db.g5
$ samtools view -bS STRAIN.sam STRAIN.bam
With these recent assemblies, I get the same error.
D. picard-tools SamFormatConverter crashes.
I have tried it with at least 3 different reference assemblies.
Could somebody please advise me?
Thanks
John
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