Question: bait interval list for picard collecthsmetrices
0
gravatar for archie
2.5 years ago by
archie100
India
archie100 wrote:

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

alignment picard exome • 2.2k views
ADD COMMENTlink modified 2.5 years ago by igor11k • written 2.5 years ago by archie100
0
gravatar for archie
2.5 years ago by
archie100
India
archie100 wrote:

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

Archana

ADD COMMENTlink written 2.5 years ago by archie100
0
gravatar for finswimmer
2.5 years ago by
finswimmer14k
Germany
finswimmer14k wrote:

Hello archie,

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

fin swimmer

ADD COMMENTlink written 2.5 years ago by finswimmer14k

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.

ADD REPLYlink written 2.5 years ago by archie100

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

ADD REPLYlink written 2.5 years ago by finswimmer14k
0
gravatar for igor
2.5 years ago by
igor11k
United States
igor11k wrote:

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.

ADD COMMENTlink written 2.5 years ago by igor11k

Hi

Thank you for the explanation .

ADD REPLYlink written 2.5 years ago by archie100

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.

ADD REPLYlink modified 21 months ago • written 21 months ago by Roman Luštrik100
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