translocation test cases

Question

translocation test cases

zeeev opened this issue 8 years ago · comments

I'm very close to adding translocation support to WHAM-GRAPHENING. I'm trying to round up some test cases in BAM format. Do you have any to share?

abolia · Answer 1 · Fri Apr 15 2016 02:41:59 GMT+0800 (China Standard Time)

Hi Zev,

Sure, I can send you some. Would you like me to upload them to GNomEx or
somewhere else. Let me know.

Thanks,
Ashini

On Wed, Apr 13, 2016 at 9:39 AM, Zev Kronenberg notifications@github.com
wrote:

@abolia https://github.com/abolia @BrettKennedy
https://github.com/BrettKennedy @ryanabo https://github.com/ryanabo,

I'm very close to adding translocation support to WHAM-GRAPHENING. I'm
trying to round up some test cases in BAM format. Do you have any to share?

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#31

Kind Regards,
Ashini Bolia

abolia · Answer 2 · Fri Apr 15 2016 02:49:19 GMT+0800 (China Standard Time)

Hey Zev,

I have uploaded 2 bams on GNomEx:

https://hci-bio-app.hci.utah.edu/gnomex/gnomexFlex.jsp?analysisNumber=A3484

Sample SP-14-15849
True Positive: ALK gene chr2:29415639-30144477
Supected Partner: EML4 gene chr2:42396477-42559688

Sample SP-14-20579
True Positive: EWSR1 gene chr22:29663997-29686672
Supected Partner: WT1 gene chr11:32409321-32457081

Let me know if you need more BAM's.

Thanks,

Ashini

On Thu, Apr 14, 2016 at 12:41 PM, Ashini Bolia abolia@asu.edu wrote:

Hi Zev,

Sure, I can send you some. Would you like me to upload them to GNomEx or
somewhere else. Let me know.

Thanks,
Ashini

On Wed, Apr 13, 2016 at 9:39 AM, Zev Kronenberg notifications@github.com
wrote:

@abolia https://github.com/abolia @BrettKennedy
https://github.com/BrettKennedy @ryanabo https://github.com/ryanabo,

I'm very close to adding translocation support to WHAM-GRAPHENING. I'm
trying to round up some test cases in BAM format. Do you have any to share?

—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
#31

Kind Regards,
Ashini Bolia

Zev Kronenberg · Answer 3 · Fri Apr 15 2016 22:56:13 GMT+0800 (China Standard Time)

@abolia Thank you. I'm trying them out now.

Zev Kronenberg · Answer 4 · Fri Apr 15 2016 23:04:31 GMT+0800 (China Standard Time)

What reference genome was used? HG19?

abolia · Answer 5 · Fri Apr 15 2016 23:09:53 GMT+0800 (China Standard Time)

Yes, hg19 was used.

Thanks,
Ashini

On Fri, Apr 15, 2016 at 9:04 AM, Zev Kronenberg notifications@github.com
wrote:

What reference genome was used? HG19?

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#31 (comment)

Kind Regards,
Ashini Bolia

Zev Kronenberg · Answer 6 · Fri Apr 15 2016 23:10:47 GMT+0800 (China Standard Time)

@abolia Looks like it is a custom reference genome. I will need your reference.

abolia · Answer 7 · Fri Apr 15 2016 23:22:34 GMT+0800 (China Standard Time)

Oh yeah, sorry I forgot to mention that. It is custom reference that
contains the phiX and adapter sponges. I uploaded the fasta, index and dict
files to GNomEx under the same analysis.

Thanks,
Ashini

On Fri, Apr 15, 2016 at 9:10 AM, Zev Kronenberg notifications@github.com
wrote:

@abolia https://github.com/abolia Looks like it is a custom reference
genome. I will need your reference.

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You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
#31 (comment)

Kind Regards,
Ashini Bolia

Zev Kronenberg · Answer 8 · Wed Apr 27 2016 06:05:32 GMT+0800 (China Standard Time)

Hi @abolia @BrettKennedy @srynobio,

WHAM-G, on the devel branch, calls BNDs (inter-chromosomal events). If you'd be interested in trying it follow the steps below. Otherwise I will let you know when a do a full release. Any feedback is welcome.

cd wham
checkout devel
make graphDebug

Here is an example of how to run it:

WHAM-GRAPHENING -e Y,MT,GL000207.1,GL000226.1,GL000229.1,GL000231.1,GL000210.1,GL000239.1,GL000235.1,GL000201.1,GL000247.1,GL000245.1,GL000197.1,GL000203.1,GL000246.1,GL000249.1,GL000196.1,GL000248.1,GL000244.1,GL000238.1,GL000202.1,GL000234.1,GL000232.1,GL000206.1,GL000240.1,GL000236.1,GL000241.1,GL000243.1,GL000242.1,GL000230.1,GL000237.1,GL000233.1,GL000204.1,GL000198.1,GL000208.1,GL000191.1,GL000227.1,GL000228.1,GL000214.1,GL000221.1,GL000209.1,GL000218.1,GL000220.1,GL000213.1,GL000211.1,GL000199.1,GL000217.1,GL000216.1,GL000215.1,GL000205.1,GL000219.1,GL000224.1,GL000223.1,GL000195.1,GL000212.1,GL000222.1,GL000200.1,GL000193.1,GL000194.1,GL000225.1,GL000192.1,NC_007605 -x 10 -a ~/shared_resources/gatk-resouces/human_g1k_v37.fasta -f CHM1_1.bam -x 5 > test 2> wham.err

After looking at you data I would highly recommend pre-trimming the reads to remove the high rate of N's. That will improve both WHAM and Delly calls.

Tjitskedv · Answer 9 · Fri Sep 08 2017 18:01:52 GMT+0800 (China Standard Time)

Hi,

I was wondering what the status is on implementing translocation detection.

regards,
Tjitske

Zev Kronenberg · Answer 10 · Tue Sep 12 2017 04:36:47 GMT+0800 (China Standard Time)

@Tjitskedv Currently, I don't have time time implement the translocation functionality. I'de be happy if someone was interested in helping.