Clean BAM Files Generated by CGATools

Tired of seeing the error "samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed."  in those .bam files you generated using CGATools.  Here's a way to remove those pesky lines that Samtools does not like.  Basically, we are going to remove any line where the cigar string fulfills any of the following:

starts with \d+N\dD
starts with \d+P
starts with \d+I
ends with \d+P

where \d+ is the Perl regular expression meaning any integer containing an unspecified number of digits.  Here is a pipeline that uses Samtools and AWK to do this for us.


Enjoy nice, clean (and hopefully problem free) .bam files.

Convert Complete Genomics Data to BAM File

Complete Genomics provides cgatools as a program suite to help manage the data they produce for investigators.  Although still in its beta form, cgatools does provide some functionality for converting evidence dnbs files (.tsv.bz2) to .bam format.  Below is a script that does so, the only caveat being that I can't seem to get the samtools depth command to work with the generated .bam files.


Here are links to documentation and a handy command reference for cgatools.

Download Complete Genomics Reference Files

A reference genome is needed when using cgatools on Complete Genomics data.  Here are links to the ftp sites that contain the reference compact randomly accessible reference (.crr) files.  Just use the wget command from a UNIX cluster to download.

NCBI Build 36:
ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr

NCBI Build 37:
ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr

The next step is to verify that the file downloaded completely.  Run one of the following commands at the command prompt depending on the version of the .crr file you downloaded.


The file output should look like this for build 36.


And this for build 37.