search

Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
404 stars 154 forks source link

Output only in stats folder but not in evidence and variants folders #196

Open oflorez opened 5 years ago

oflorez commented 5 years ago

Dear manta team, I am using manta hoping I can detect a deletion of a whole gene of about 20 kb using WXS bam files. Considering that the sequence dictionary (SQ header lines) contained entries for everything, I only keep the one interested me (chr1) and I also use chr1_hg38.fasta for the analysis. I did this because it always appear a configuration error where fasta file is missing a chromosome found in bam file or vice-verse.

I have multiple bam files and I ran this command (example for 3 bam files): configManta.py --bam=sample1.bam --bam=sample2.bam --bam=sample3.bam --referenceFasta=chr1_hg38.fasta --exome --region=chr1 --runDir=manta_analysis_chr1/

It gave me this message:

Successfully created workflow run script. To execute the workflow, run the following script and set appropriate options: /manta_analysis_chr1/runWorkflow.py

which I ran, but I have not output VCF files as expected. In the workflow.error.log.txt file there is an error related with WorkflowRunner. Please find attached this file.

I really appreciate any help in this matter. workflow.error.log.txt

x-chen commented 4 years ago

The error is likely due to some reads aligned in chr1 are split-aligned, or their mate reads are chimerically aligned, to some chromosome other than chr1.

Manta does require the bam header and the input reference are consistent. To solve the problem, you could use the original bam file, and specify the reference genome used for alignment to the option referenceFasta. It's fine to use "--region=chr1" to limit the analysis on chr1.