Incorporate Bis-SNP into bisulfite-sequencing pipeline

GoogleCodeExporter commented 8 years ago

Yaping has developed and tested a tool, Bis-SNP, to determine genotypes from 
whole-genome bisulfite-seq (WGBS) sequences.  It works best on several combined 
lanes of sequence (10x coverage), but can yield valuable information from a 
single lane. I'd like it to be run by default on bisulfite-seq and NOMe-seq 
lanes.  Consult with Yaping if we need to set different parameters for WGBS and 
NOMe-seq.  Also, there is an online user manual, please link to this in the 
"description" field.

This is important for our TCGA sequence analysis pipeline, so it is very high 
priority to start running it and seeing if we run into any problems.

Original issue reported on code.google.com by benb...@gmail.com on 12 Sep 2011 at 4:05

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 12 Sep 2011 at 6:41

Changed state: Accepted
Added labels: Project-NGS-bisulfiteSeqPipeline

GoogleCodeExporter commented 8 years ago

Where can I get a working bin for this, and how do I run it?

Original comment by zack...@gmail.com on 19 Sep 2011 at 9:52

GoogleCodeExporter commented 8 years ago

Hi, zack, you can download the binary jar file and User Manual from this link:
http://epigenome.usc.edu/publicationdata/bissnp2011/

and the source code is available here:
https://uecgatk.svn.sourceforge.net/svnroot/uecgatk/
trunk/src/edu/usc/epigenome/uecgatk/bisulfitesnpmodel

Original comment by lyping1...@gmail.com on 19 Sep 2011 at 10:41

GoogleCodeExporter commented 8 years ago

great! 

I was going to download it and work with you on getting a good default set of 
arguments but hpcc is down, so none of the files are available.

Original comment by zack...@gmail.com on 19 Sep 2011 at 10:47

GoogleCodeExporter commented 8 years ago

I have it in the pipeline, but i have hardcoded PE "-pem" into the call, so it 
fails on SR bams. is it possible to make it determine PE/SR by itself?

Original comment by zack...@gmail.com on 16 Feb 2012 at 12:12

Changed state: Started

GoogleCodeExporter commented 8 years ago

yes, I think so. I will change it to recognize PE/SE.Thanks

Original comment by lyping1...@gmail.com on 16 Feb 2012 at 12:20

GoogleCodeExporter commented 8 years ago

added to production pipeline, lets see how it does over the next few runs.

Original comment by zack...@gmail.com on 4 Apr 2012 at 7:12

Changed state: Ongoing

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 4 Apr 2012 at 7:12

Added labels: Priority-High

GoogleCodeExporter commented 8 years ago

Can we run this on merged lanes?   The most important are the TCGA merges.  But 
NOMe-seq libraries will sometimes be multiple lanes as well.

The approved TCGA output for Bis-SNP is still being determined.  But I think we 
should generate the following "modified wiggle" format for the time being (CpG 
only).

track type=wiggle_0 name=sample alwaysZero=off
variableStep chrom=chr1
469     25    4
480     80    10
800     88    8

Where the first two fields are standard wiggle (field1=genomic
coordinate, field2=percent methylated), and field3 is the total number
of (C or T) reads covering the position.

Original comment by benb...@gmail.com on 4 Apr 2012 at 7:21

GoogleCodeExporter commented 8 years ago

For merged lanes, you could specify -I lane_1.bam -I lane_2.bam.... multiple 
times. But if different lanes bam file own different Readgroup name, then 
BisSNP right now would call them separately as different samples. How is the 
Read group name signed to bam file, by lane name or sample name?
For "modified wiggle" format, I already made a perl script to convert from VCF 
file generated by BisSNP.

Original comment by lyping1...@gmail.com on 4 Apr 2012 at 8:58

GoogleCodeExporter commented 8 years ago

Here is my perl scripts to convert from VCF to wiggle or modified wiggle file:
http://epigenome.usc.edu/publicationdata/bissnp2011/vcf2cpg_wig_file.pl
http://epigenome.usc.edu/publicationdata/bissnp2011/vcf2cpg_wig_plus_file.pl

Original comment by lyping1...@gmail.com on 4 Apr 2012 at 10:19

GoogleCodeExporter commented 8 years ago

our latest attempt didnt seem to work, heres the errors:

/home/uec-00/shared/production/software/java/default/bin/java -Xmx20G -jar 
/home/uec-00/shared/production/software/bissnp/bissnp-default.jar -aecm -R 
/home/uec-00/shared/production/genomes/hg19_rCRSchrm/hg19_rCRSchrm.fa -T 
BisulfiteGenotyper -I ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam 
-D /home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf -vfn1 
ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam.cpg.raw.vcf -vfn2 
ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam.snp.raw.vcf 
-stand_call_conf 30 -stand_emit_conf 0 -L 
/home/uec-00/shared/production/software/bissnp/wholegenome_interval_list.hg19.be
d -out_modes DEFAULT_FOR_TCGA -single_sample normal_test -nt 5 -rgv hg19 -mbq 0 
-mmq 30
##### ERROR 
--------------------------------------------------------------------------------
----------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error 
occurred during the traversal.
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.getTraversalError(HierarchicalMicroScheduler.java:356)
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:246)
    at edu.usc.epigenome.uecgatk.BisSNP.BisSNP.execute(BisSNP.java:275)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    at edu.usc.epigenome.uecgatk.BisSNP.BisSNP.main(BisSNP.java:134)
Caused by: java.lang.IllegalArgumentException: Duplicate allele added to 
VariantContext: A
    at org.broadinstitute.sting.utils.variantcontext.VariantContext.makeAlleles(VariantContext.java:1182)
    at org.broadinstitute.sting.utils.variantcontext.VariantContext.<init>(VariantContext.java:277)
    at org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:392)
    at edu.usc.epigenome.uecgatk.BisSNP.BisulfiteGenotyperEngine.createVariantContextFromLikelihoods(BisulfiteGenotyperEngine.java:574)
    at edu.usc.epigenome.uecgatk.BisSNP.BisulfiteGenotyperEngine.calculateLikelihoods(BisulfiteGenotyperEngine.java:175)
    at edu.usc.epigenome.uecgatk.BisSNP.BisulfiteGenotyperEngine.calculateLikelihoodsAndGenotypes(BisulfiteGenotyperEngine.java:138)
    at edu.usc.epigenome.uecgatk.BisSNP.BisulfiteGenotyperEngine.<init>(BisulfiteGenotyperEngine.java:104)
    at edu.usc.epigenome.uecgatk.BisSNP.BisulfiteGenotyper.map(BisulfiteGenotyper.java:328)
    at edu.usc.epigenome.uecgatk.BisSNP.BisulfiteGenotyper.map(BisulfiteGenotyper.java:1)
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
    at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:72)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:619)
##### ERROR 
--------------------------------------------------------------------------------
----------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.5-3-gbb2c10b):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation 
http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions 
http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: An error occurred during the traversal.
##### ERROR 
--------------------------------------------------------------------------------
----------
mv: cannot stat 
`ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam.cpg.raw.vcf': No such 
file or directory
mv: cannot stat 
`ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam.snp.raw.vcf': No such 
file or directory
----------------------------------------
Begin PBS Prologue Fri Apr  6 22:46:02 PDT 2012
Job ID:            1383711.hpc-pbs.usc.edu
Username:          ramjan
Group:             hsc-ar
Name:              
uec_C02APACXX_C02APACXX_5_NIC1254A13_uscec_bissnp663669832097810418.sh
Queue:             laird_exe
Shared Access:     yes
Nodes:             hpc2701 
TMPDIR:            /tmp/1383711.hpc-pbs.usc.edu
End PBS Prologue Fri Apr  6 22:46:02 PDT 2012
----------------------------------------
INFO  22:46:06,397 RodBindingArgumentTypeDescriptor - Dynamically determined 
type of 
/home/uec-00/shared/production/software/bissnp/wholegenome_interval_list.hg19.be
d to be BED 
INFO  22:46:06,437 HelpFormatter - 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------- 
INFO  22:46:06,437 HelpFormatter - The Bis-SNP-0.54, Compiled 2012/03/14 
15:25:14 
INFO  22:46:06,438 HelpFormatter - Based on The Genome Analysis Toolkit (GATK) 
v1.5-3-gbb2c10b (prebuild GATK package could be download here: 
ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTK-1.5-3-gbb
2c10b.tar.bz2) 
INFO  22:46:06,438 HelpFormatter - Copyright (c) 2011 USC Epigenome Center 
INFO  22:46:06,438 HelpFormatter - Please view our documentation at 
http://epigenome.usc.edu/publicationdata/bissnp2011/ 
INFO  22:46:06,438 HelpFormatter - For support, please send email to 
lyping1986@gmail.com or benbfly@gmail.com 
INFO  22:46:06,439 HelpFormatter - Program Args: -aecm -R 
/home/uec-00/shared/production/genomes/hg19_rCRSchrm/hg19_rCRSchrm.fa -T 
BisulfiteGenotyper -I ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam 
-D /home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf -vfn1 
ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam.cpg.raw.vcf -vfn2 
ResultCount_C02APACXX_5_NIC1254A13.hg19_rCRSchrm.fa.bam.snp.raw.vcf 
-stand_call_conf 30 -stand_emit_conf 0 -L 
/home/uec-00/shared/production/software/bissnp/wholegenome_interval_list.hg19.be
d -out_modes DEFAULT_FOR_TCGA -single_sample normal_test -nt 5 -rgv hg19 -mbq 0 
-mmq 30 
INFO  22:46:06,439 HelpFormatter - Date/Time: 2012/04/06 22:46:06 
INFO  22:46:06,439 HelpFormatter - 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------- 
INFO  22:46:06,439 HelpFormatter - 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------- 
INFO  22:46:06,494 RodBindingArgumentTypeDescriptor - Dynamically determined 
type of /home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf 
to be VCF 
INFO  22:46:06,540 GenomeAnalysisEngine - Strictness is SILENT 
INFO  22:46:06,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  22:46:06,693 SAMDataSource$SAMReaders - Done initializing BAM readers: 
total time 0.06 
INFO  22:46:06,745 RMDTrackBuilder - Loading Tribble index from disk for file 
/home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf 
INFO  22:46:06,994 MicroScheduler - Running the GATK in parallel mode with 5 
concurrent threads 
sample name provided was masked by bam file header
INFO  22:46:07,738 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  22:46:07,748 SAMDataSource$SAMReaders - Done initializing BAM readers: 
total time 0.01 
INFO  22:46:07,748 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  22:46:07,756 SAMDataSource$SAMReaders - Done initializing BAM readers: 
total time 0.01 
INFO  22:46:07,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  22:46:07,762 RMDTrackBuilder - Loading Tribble index from disk for file 
/home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf 
INFO  22:46:07,766 SAMDataSource$SAMReaders - Done initializing BAM readers: 
total time 0.01 
INFO  22:46:07,768 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  22:46:07,775 SAMDataSource$SAMReaders - Done initializing BAM readers: 
total time 0.01 
INFO  22:46:07,900 RMDTrackBuilder - Loading Tribble index from disk for file 
/home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf 
INFO  22:46:08,042 RMDTrackBuilder - Loading Tribble index from disk for file 
/home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf 
INFO  22:46:08,080 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL 
STARTING] 
INFO  22:46:08,081 TraversalEngine -        Location processed.sites  runtime 
per.1M.sites completed total.runtime remaining 
INFO  22:46:08,216 RMDTrackBuilder - Loading Tribble index from disk for file 
/home/uec-00/shared/production/software/bissnp/dbsnp_135.hg19.sort.vcf 
INFO  22:46:37,743 TraversalEngine -    chr1:2710500        2.64e+06   30.0 s   
    11.3 s      0.1%         9.5 h     9.5 h 
INFO  22:47:07,750 TraversalEngine -    chr1:5585622        5.59e+06   60.0 s   
    10.7 s      0.2%         9.2 h     9.2 h 
INFO  22:47:37,755 TraversalEngine -    chr1:8247405        8.18e+06   90.0 s   
    11.0 s      0.3%         9.4 h     9.4 h 
INFO  22:48:07,769 TraversalEngine -   chr1:10621431        1.06e+07    2.0 m   
    11.3 s      0.3%         9.7 h     9.7 h 
INFO  22:48:39,245 TraversalEngine -   chr1:13150138        1.32e+07    2.5 m   
    11.5 s      0.4%         9.9 h     9.9 h 
INFO  22:49:09,249 TraversalEngine -   chr1:15975977        1.59e+07    3.0 m   
    11.4 s      0.5%         9.8 h     9.7 h 
INFO  22:49:39,250 TraversalEngine -   chr1:18643493        1.86e+07    3.5 m   
    11.3 s      0.6%         9.8 h     9.7 h 
INFO  22:50:09,314 TraversalEngine -   chr1:21432550        2.14e+07    4.0 m   
    11.3 s      0.7%         9.7 h     9.6 h 
INFO  22:50:39,319 TraversalEngine -   chr1:24130765        2.41e+07    4.5 m   
    11.3 s      0.8%         9.7 h     9.6 h 
INFO  22:51:09,329 TraversalEngine -   chr1:26944835        2.69e+07    5.0 m   
    11.2 s      0.9%         9.6 h     9.5 h 
INFO  22:51:39,338 TraversalEngine -   chr1:29504333        2.95e+07    5.5 m   
    11.3 s      1.0%         9.7 h     9.6 h 
INFO  22:52:09,344 TraversalEngine -   chr1:32328057        3.23e+07    6.0 m   
    11.2 s      1.0%         9.6 h     9.5 h 
INFO  22:52:39,506 TraversalEngine -   chr1:34237024        3.42e+07    6.5 m   
    11.5 s      1.1%         9.8 h     9.7 h 
INFO  22:53:09,514 TraversalEngine -   chr1:36027788        3.60e+07    7.0 m   
    11.7 s      1.2%        10.1 h     9.9 h 
INFO  22:53:39,519 TraversalEngine -   chr1:38001595        3.80e+07    7.5 m   
    11.9 s      1.2%        10.2 h    10.1 h 
INFO  22:54:09,529 TraversalEngine -   chr1:39818841        3.98e+07    8.0 m   
    12.1 s      1.3%        10.4 h    10.3 h 
INFO  22:54:39,531 TraversalEngine -   chr1:41606632        4.16e+07    8.5 m   
    12.3 s      1.3%        10.6 h    10.4 h 
INFO  22:55:09,534 TraversalEngine -   chr1:43542858        4.35e+07    9.0 m   
    12.5 s      1.4%        10.7 h    10.5 h 
INFO  22:55:39,539 TraversalEngine -   chr1:45354667        4.53e+07    9.5 m   
    12.6 s      1.5%        10.8 h    10.7 h 
INFO  22:56:09,546 TraversalEngine -   chr1:47229869        4.72e+07   10.0 m   
    12.8 s      1.5%        11.0 h    10.8 h 
INFO  22:56:39,551 TraversalEngine -   chr1:49870264        4.99e+07   10.5 m   
    12.7 s      1.6%        10.9 h    10.7 h 
INFO  22:57:09,558 TraversalEngine -   chr1:52484622        5.25e+07   11.0 m   
    12.6 s      1.7%        10.8 h    10.7 h 
INFO  22:57:39,559 TraversalEngine -   chr1:55214423        5.51e+07   11.5 m   
    12.5 s      1.8%        10.8 h    10.6 h 
INFO  22:58:09,565 TraversalEngine -   chr1:57816667        5.78e+07   12.0 m   
    12.5 s      1.9%        10.7 h    10.5 h 
INFO  22:58:39,573 TraversalEngine -   chr1:60454929        6.04e+07   12.5 m   
    12.4 s      2.0%        10.7 h    10.5 h 
INFO  22:59:09,585 TraversalEngine -   chr1:62907695        6.29e+07   13.0 m   
    12.4 s      2.0%        10.7 h    10.5 h 
INFO  22:59:39,592 TraversalEngine -   chr1:65542888        6.55e+07   13.5 m   
    12.4 s      2.1%        10.7 h    10.4 h 
INFO  23:00:09,596 TraversalEngine -   chr1:68135480        6.81e+07   14.0 m   
    12.4 s      2.2%        10.6 h    10.4 h 
INFO  23:00:39,605 TraversalEngine -   chr1:70721697        7.07e+07   14.5 m   
    12.3 s      2.3%        10.6 h    10.4 h 
INFO  23:01:09,612 TraversalEngine -   chr1:73358824        7.33e+07   15.0 m   
    12.3 s      2.4%        10.6 h    10.3 h 
INFO  23:01:39,620 TraversalEngine -   chr1:75927316        7.59e+07   15.5 m   
    12.3 s      2.5%        10.6 h    10.3 h 
INFO  23:02:09,622 TraversalEngine -   chr1:78185855        7.81e+07   16.0 m   
    12.3 s      2.5%        10.6 h    10.3 h 
INFO  23:02:39,633 TraversalEngine -   chr1:80810012        8.07e+07   16.5 m   
    12.3 s      2.6%        10.6 h    10.3 h 
INFO  23:03:09,639 TraversalEngine -   chr1:83403010        8.34e+07   17.0 m   
    12.3 s      2.7%        10.5 h    10.3 h 
INFO  23:03:39,641 TraversalEngine -   chr1:86048398        8.60e+07   17.5 m   
    12.2 s      2.8%        10.5 h    10.2 h 
INFO  23:04:09,649 TraversalEngine -   chr1:88633678        8.86e+07   18.0 m   
    12.2 s      2.9%        10.5 h    10.2 h 
INFO  23:04:39,657 TraversalEngine -   chr1:91278075        9.12e+07   18.5 m   
    12.2 s      2.9%        10.5 h    10.2 h 
INFO  23:05:09,660 TraversalEngine -   chr1:93901066        9.38e+07   19.0 m   
    12.2 s      3.0%        10.5 h    10.1 h 
INFO  23:05:39,668 TraversalEngine -   chr1:96466450        9.64e+07   19.5 m   
    12.2 s      3.1%        10.4 h    10.1 h 
INFO  23:06:09,675 TraversalEngine -   chr1:98925683        9.89e+07   20.0 m   
    12.1 s      3.2%        10.4 h    10.1 h 
INFO  23:06:39,685 TraversalEngine -  chr1:101521303        1.01e+08   20.5 m   
    12.1 s      3.3%        10.4 h    10.1 h 
INFO  23:07:09,687 TraversalEngine -  chr1:104369450        1.04e+08   21.0 m   
    12.1 s      3.4%        10.4 h    10.0 h 
INFO  23:07:39,692 TraversalEngine -  chr1:107070337        1.07e+08   21.5 m   
    12.1 s      3.5%        10.4 h    10.0 h 
INFO  23:08:09,695 TraversalEngine -  chr1:109751064        1.10e+08   22.0 m   
    12.0 s      3.5%        10.4 h    10.0 h 
INFO  23:08:39,702 TraversalEngine -  chr1:112503552        1.13e+08   22.5 m   
    12.0 s      3.6%        10.3 h    10.0 h 
INFO  23:09:09,711 TraversalEngine -  chr1:114993168        1.15e+08   23.0 m   
    12.0 s      3.7%        10.3 h    10.0 h 
INFO  23:09:39,716 TraversalEngine -  chr1:117709031        1.18e+08   23.5 m   
    12.0 s      3.8%        10.3 h     9.9 h 
INFO  23:10:09,723 TraversalEngine -  chr1:120322387        1.20e+08   24.0 m   
    12.0 s      3.9%        10.3 h     9.9 h 
----------------------------------------
Begin PBS Epilogue Fri Apr  6 23:10:28 PDT 2012
Job ID:           1383711.hpc-pbs.usc.edu
Username:         ramjan
Group:            hsc-ar
Job Name:         
uec_C02APACXX_C02APACXX_5_NIC1254A13_uscec_bissnp663669832097810418.sh
Session:          15789
Limits:           
mem=15000mb,neednodes=1:ppn=12:hexcore,nodes=1:ppn=12:hexcore,walltime=200:00:00
Resources:        cput=02:06:05,mem=8719356kb,vmem=21805572kb,walltime=00:24:26
Queue:            laird_exe
End PBS Epilogue Fri Apr  6 23:10:28 PDT 2012
----------------------------------------

Original comment by zack...@gmail.com on 8 Apr 2012 at 5:37

GoogleCodeExporter commented 8 years ago

 I have not met such an error in the previous test..could u give me the bam file location? so that i could test it again by myself. Thanks.

Original comment by lyping1...@gmail.com on 10 Apr 2012 at 12:09

GoogleCodeExporter commented 8 years ago

And just a reminder, "-single_sample normal_test" should not be specified in 
the latest version. you could use -nt 12 (8g-10g in total), rather than 3g per 
thread.

Original comment by lyping1...@gmail.com on 10 Apr 2012 at 4:27

GoogleCodeExporter commented 8 years ago

bissnp has been a working part of our bis pipeline for a while now. closing 
this ticket

Original comment by zack...@gmail.com on 30 Jul 2012 at 8:30

Changed state: Fixed

GoogleCodeExporter commented 8 years ago

I am encountering this same error using the latest version of bssnp. It looks 
like this bug was fixed in one of the later versions of GATK, but bissnp is 
still build upon an older one.

Original comment by zynd...@gmail.com on 3 Dec 2012 at 8:17

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 3 Dec 2012 at 8:23

Changed state: Started

GoogleCodeExporter commented 8 years ago

"Incorporate Bis-SNP into bisulfite-sequencing pipeline" has been accomplished 
for some time, closing

Original comment by zack...@gmail.com on 3 Jan 2014 at 10:14

Changed state: Done

uec / Issue.Tracker

Incorporate Bis-SNP into bisulfite-sequencing pipeline #151