gatk-3.8

Commit Graph

Author	SHA1	Message	Date
kshakir	83e207d9dd	Added option to exclude intervals during chunk calling. Removed job priority as temp space isn't as tight at the moment and planning on changing the priority interface. Updated chunk calling with ebanks: - Using "the bundle" of resources. - Using dbsnp 132 and 1000G indel RODs for both RTC & IR. - Using the default maxIntervalSize in RTC. - Removed use of UG.exactCalculation argument. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5814 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-18 03:48:02 +00:00
kshakir	95fc6c0a83	Changed VR tranches from old 0.1-10 to new 100 to 90. Using hapmap training and truth based on wiki. Explicitly setting the ts_filter_level even though 99.0 is the default. Recal file path now ends with with .recal. Added ar's vcf input. Omni rod name now omni instead of 1kg. The VR RodBind tags had spaces in them. Was passing both the full intervals and the chunk intervals to chunk jobs. Switched back to chr20 for default since the VR crashes on small intervals sets with "MESSAGE: Matrix is singular." Log files names based on the file paths + .out. Added eval statifications by sample based on the Hybrid Selection / Whole Exome pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5800 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-13 14:38:56 +00:00
kshakir	08c13f3944	Using embedded GATK. Hardcoded the reference and dbsnp since the training rods are also hardcoded, for now. Changed freeze/chr20 to wg/chr20/cent1 to also test the heaviest known shard. Other cleanup. TODO: Memory command line options or have the script figure it out using FLS or similar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5799 348d0f76-0448-11de-a6fe-93d51630548a	2011-05-12 23:19:49 +00:00

Author

SHA1

Message

Date

kshakir

83e207d9dd

Added option to exclude intervals during chunk calling.

Removed job priority as temp space isn't as tight at the moment and planning on changing the priority interface.
Updated chunk calling with ebanks:
- Using "the bundle" of resources.
- Using dbsnp 132 and 1000G indel RODs for both RTC & IR.
- Using the default maxIntervalSize in RTC.
- Removed use of UG.exactCalculation argument.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5814 348d0f76-0448-11de-a6fe-93d51630548a

2011-05-18 03:48:02 +00:00

kshakir

95fc6c0a83

Changed VR tranches from old 0.1-10 to new 100 to 90.

Using hapmap training and truth based on wiki.
Explicitly setting the ts_filter_level even though 99.0 is the default.
Recal file path now ends with with .recal.
Added ar's vcf input.
Omni rod name now omni instead of 1kg.
The VR RodBind tags had spaces in them.
Was passing both the full intervals and the chunk intervals to chunk jobs.
Switched back to chr20 for default since the VR crashes on small intervals sets with "MESSAGE: Matrix is singular."
Log files names based on the file paths + .out.
Added eval statifications by sample based on the Hybrid Selection / Whole Exome pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5800 348d0f76-0448-11de-a6fe-93d51630548a

2011-05-13 14:38:56 +00:00

kshakir

08c13f3944

Using embedded GATK.

Hardcoded the reference and dbsnp since the training rods are also hardcoded, for now.
Changed freeze/chr20 to wg/chr20/cent1 to also test the heaviest known shard.
Other cleanup.
TODO: Memory command line options or have the script figure it out using FLS or similar.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5799 348d0f76-0448-11de-a6fe-93d51630548a

2011-05-12 23:19:49 +00:00

3 Commits (a38b2be329bc020158082ea6f81c5eb066b83e88)