Agilent SureSelect exome enrichment bed file

[vishnuamaram]

Hey yl01 & jjmmi,

I hope you guys are experts in NGS,especially exome sequencing by now.

I am a kind of amateur and little expert, did part of analysis of my exome data.

This is what i followed til now.

a) alignment by BWA
b) convert to BAM, sort, index using samtools
c) remove pcr duplicates by picard.
d) next i need to use GATK for indel recalibration, BQSR & i am not sure of how to implement this agilent exon bed file at this stage of analysis.

Hope you guys could help me out from my (d) step onwards, kindly respond to me in detail.

Thank you,
Vishnu.

[vishnuamaram]

Hey yl01 & jjmmi,

I hope you guys are experts in NGS,especially exome sequencing by now.

I am a kind of amateur and little expert, did part of analysis of my exome data.

This is what i followed til now.

a) alignment by BWA
b) convert to BAM, sort, index using samtools
c) remove pcr duplicates by picard.
d) next i need to use GATK for indel recalibration, BQSR & i am not sure of how to implement this agilent exon bed file at this stage of analysis.

Hope you guys could help me out from my (d) step onwards, kindly respond to me in detail.

Thank you,
Vishnu.

[yl01]

Can I also find them if I haven't made a design myself?

I have some exome data from collagues enriched with SureSelect v4, sequenced by BGI. Can I just download the designfiles somewhere from the Agilent website, without logging in?

You don't need a design by yourslef to get the files of SureSelect v4. You just need to login to the SureDesign web site. The account is free. If you can download the files from somewhere else, I don't know.

[ddaneels]

Can I also find them if I haven't made a design myself?

I have some exome data from collagues enriched with SureSelect v4, sequenced by BGI. Can I just download the designfiles somewhere from the Agilent website, without logging in?

[jjmmii]

I found it, thank you so much!
For anyone interested, after logging in to SureDesign, click on "Find Designs" and choose your kit, then you will be able to see the default catalogs for download.

[yl01]

The .bed files are available in SureDesign website. You can find the link of it on eArray entry page. Your eArray login can be used to login to SureDesign. When you have the .bed files, you will see the tracks.

[jjmmii]

This is an old topic, but I think you should use the "Target Regions" for variant calling in GATK, as the GATK walkers will not want to look at just the probes or covered probes when calling variants from the entire exome. I am also looking for this .bed file in eArray, but I get only one file titled "RNA Capture Human Kinome" following instructions from http://www.biostars.org/p/5187/#18071 . May you please let me know how you found the "Target Regions" track?

[yl01]

Got the answer from Agilent informatics support. The bed files are available from SureDesign web site, which can be seen from the eArray entry page. The downloaded bed files have 3 tracks: "Target Regions", "Probes" and "Covered Probes". Now the question is which one of these should be used as the exome target file for variant calling programs e.g. GATK?

[yl01]

I was wondering where can I donwload the bed file for the Agilent SureSelect exome enrichment for human. Someone has mentioned eArray web site. Doesn anyone know what keywords should I use to find the correct array design in eArray? Or I can get it from somewhere else?