capmq and verifybamid

Question

[Peter Chung]

Hello, I am new in tackling the containmation issues in bam files.I used below packages to do so:

capmq: 
https://github.com/mcshane/capmq
verifybamid: 
https://genome.sph.umich.edu/wiki/VerifyBamID

First I used the capmq modules to limit the highest mapping quality to 30 bam files:

capmq -C30 input.bam

and then I run the GATK to output the vcf files and then use

verifyBamID --vcf {input.vcf} --bam {input.bam} --smID {params.smID} --out {output} --best 

However, all my sequencing results FREEMIX values are larger than the >1%, which are failed. So what should I do to decrease the FREEMIX values or is there any others packages can tackle the containmation issues. Please advice, thanks.

[GenoMax]

tackling the index hopping issues in bam files

I guess you are trying to identify contamination/sample swap(?) rather than index hopping. index hopping means something different and happens at the time of sequencing where a read may be misassigned to a sample it does not belong to (LINK).

I don't think what you are doing above is going to address index hopping (if that is what you are interested in). Index hopping did not become a significant issue (which can be minimized with some care) until patterned flowcells started being used.

[Peter Chung]

Yes, you are correct, I am dealing with the containmation issues, and after the capmq package, I still can not lower the FREEMIX value to meet the criteria. I am wondering how to lower the FREEMIX value or I should use other packages to detect containmation ? thanks.