Hi guys,
Contra has a new update (v2.0.4) -- see contra-cnv.sf.net. Here are my answers to some commonly asked questions:
1) error: /buf/chrxx.txt
This is due to the bam files NOT containing reads on a chromosome that is defined in the BED file. E.g. 10,000 regions on Chr12 are defined in the target bed file, but the bam file has no read mapped to Chr12.
In most cases, this is due to a truncated, corrupted bam file. So I have not "fixed" the script logic. Rather I am just catching this error and outputing an error message in the latest version.
2) WARNING chrxx not found. & EMPTY VCF FILE
In fasta/bam files where chromosome names have been defined with "chr" prefix, some times the script would fail. This has been fixed -- thx Eric Ho for pointing this out. This *should* fix the empty vcf file issue for some of you... let me know if it doesn't.
3) baseline.py error...
i haven't been able to catch the same error as reported by some of you. but perhaps point 1 about is relevant.. so check the bam files for presence of all chromosomes.
4) false positive/negative rates..
at exon level, the FPR is high. I have a script to detect gene-level gains and losses, and works well one some of our in house data. If you are interested, let me know.
Best wishes,
Jason
Contra has a new update (v2.0.4) -- see contra-cnv.sf.net. Here are my answers to some commonly asked questions:
1) error: /buf/chrxx.txt
This is due to the bam files NOT containing reads on a chromosome that is defined in the BED file. E.g. 10,000 regions on Chr12 are defined in the target bed file, but the bam file has no read mapped to Chr12.
In most cases, this is due to a truncated, corrupted bam file. So I have not "fixed" the script logic. Rather I am just catching this error and outputing an error message in the latest version.
2) WARNING chrxx not found. & EMPTY VCF FILE
In fasta/bam files where chromosome names have been defined with "chr" prefix, some times the script would fail. This has been fixed -- thx Eric Ho for pointing this out. This *should* fix the empty vcf file issue for some of you... let me know if it doesn't.
3) baseline.py error...
i haven't been able to catch the same error as reported by some of you. but perhaps point 1 about is relevant.. so check the bam files for presence of all chromosomes.
4) false positive/negative rates..
at exon level, the FPR is high. I have a script to detect gene-level gains and losses, and works well one some of our in house data. If you are interested, let me know.
Best wishes,
Jason
Comment