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bait interval list for picard collecthsmetrices

Dear all,

I have some samples of exome sequences. I need to check the exome capture efficiency using picard collectHsmetrcies for each sample. I have target interval list with me. but I do not have idea about the bait interval list? Should I create from the bam file -> bed file -> interval ? Or what else I should do to get this bait interval list ? I just want to sure before doing it for the accuracy in method.

I will appreciate all the suggestions

Thank you

Archana

picard alignment exome
• 8,733 views • link
updated by Arton • Arton • written by Omics data mining Omics data mining

Dear all

I am new in area of exome study.

Just now found this detail related to bait and target file for the prediction of collecthsmetrices

Bait interval = All tracks bed file (given by sequencing team) ;;;;; Target interval = covered bed file (from bam file)

Can anybody correct me here if it is right or wrong ?? . I just want to be sure for my workflow wether It is correct or not before proceeding for the analysis?

Thank you in advance

• 1 views • link
written by Omics data mining Omics data mining

Hello, If we need to calculate the coverage of coding regions of a single gene from exome data, should we change the target interval file to the gene coding positions?

• 0 views • link
written by Arton • Arton

2 answers

Target intervals are the regions or exons you are trying to capture. You don't necessarily expect to pick up all the exons, since baits/probes can't be designed for every region.

Bait intervals are the regions that correspond to the capture probes. In an ideal situation, all probes should work.

For the purpose of overall QC stats, the two should be roughly similar, but there are differences.

• 1 views • link
written by igor igor

Can you cite any references about this? I noticed that terminology regarding regions, targets, baits, "covered" regions... has much room for improvement between kit and tool providers. I think BaitDesigner might give some insight into this - it also supports your answer.

• 1 views • link
written by Roman Luštrik Roman Luštrik

Hello archie,

it is fine to use the same file for bait and target intervals.

fin swimmer

• 1 views • link
written by finswimmer finswimmer

Hi

Thank you. I am going to use the same file and will check result. I have another point in mind i.e bam input should be duplicate removed or CollectHSmetrices will automatically check for the duplicate level and count them separately ?? If no, then Can I give input of markduplicate where duplciate will be removed from bam file during processing.

• 1 views • link
written by Omics data mining Omics data mining

Hello,

there is no need to remove duplicates from bam file if you've already marked them using MarkDuplicates. CollectHSmetrics recognize is and you would also get metrics about about the level of duplications.

fin swimmer

• 1 views • link
written by finswimmer finswimmer

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