SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
input BAM files for GATK Jane M Bioinformatics 26 07-30-2015 10:58 PM
multiple BAM GATK unifiedgenotyper output memento Bioinformatics 0 02-22-2012 09:12 AM
GATK pileup with merged BAM files yxl Bioinformatics 0 04-22-2011 08:07 PM
GATK calling Merged Bam files jayce_ocean Bioinformatics 3 03-16-2011 01:15 AM
missing header information in bam cause GATK unifiedgenotyper fail foxyg Bioinformatics 3 11-11-2010 10:37 AM

Reply
 
Thread Tools
Old 03-01-2012, 05:16 PM   #1
nguyendofx
Member
 
Location: CA

Join Date: May 2011
Posts: 31
Default GATK -T UnifiedGenotyper on multipel BAM files

Dear All,

I have three BAM files, want to cal variant all together. Here is a command I used:

#java -Xmx4g -jar ~/GenomeAnalysisTK.jar -T UnifiedGenotyper -glm BOTH \
-R ~/hg19.GATK.fasta
-I Test1.recal.bam -I Test2.recal.bam -I Test3.recal.bam
-L /pipeline/resources/hg19.trueseq_exome_60mb_interval.bed
--dbsnp dbSNP.vcf
-stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 100 -l INFO -A AlleleBalance -A DepthOfCoverage -A FisherStrand
-log testRun2/rawvariants.log -o testRun2/rawvariants.vcf &

===== It work! === Here is part of the rawvariants.vcf ===

...
##contig=<ID=Y,length=59373566,assembly=hg19>
##reference=./annovar/hg19.GATK.fasta
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Homo_sapiens
1 14522 . G A 205.95 PASS AB=0.848;AC=1;AF=0.50;AN=2;BaseQRankSum=3.916;DP=125;Dels=0.00;FS=35.803;HRun=0;HaplotypeScore=1.6281;MQ=60.68;MQ0=0;MQRankSum=-1.207;QD=1.65;ReadPosRankSum=3.462 GT:AD P:GQ:PL 0/1:106,19:125:99:236,0,2845
1 14542 . A G 658.84 PASS AB=0.732;AC=1;AF=0.50;AN=2;BaseQRankSum=3.814;DP=127;Dels=0.00;FS=81.180;HRun=1;HaplotypeScore=4.7173;MQ=51.24;MQ0=0;MQRankSum=-2.094;QD=5.19;ReadPosRankSum=3.912 GT:ADP:GQ:PL 0/1:93,34:127:99:689,0,2561

....


There problem here is it doesn't report all three samples in every position (E.g 0/1:93,34:127:99:689,0,2561 on the last column)


I like to generate a vcf like this one, which has test1, test2 test3 on last three columns
....

##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test1 test2 test3
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2


Thanks,
Ng
nguyendofx is offline   Reply With Quote
Old 03-22-2012, 04:56 AM   #2
hanifk
Member
 
Location: China

Join Date: Oct 2010
Posts: 18
Default

different sample should have different RG
It seems that all your three samples have the same RG,so GATK treat them as one group.
hanifk is offline   Reply With Quote
Old 04-23-2012, 10:32 AM   #3
nguyendofx
Member
 
Location: CA

Join Date: May 2011
Posts: 31
Default

Hi Hanifk,

Thanks, I managed to get it work. Its required a distinct RG for each samples.
nguyendofx is offline   Reply With Quote
Old 04-25-2012, 02:27 AM   #4
neha
Member
 
Location: kolkata

Join Date: Oct 2011
Posts: 32
Default

Hello everyone,

I have exome data from SOLiD 5500. I am doing variant analysis using GATK UnifiedGenotyper module. The parameters I use are

java -jar ./../GenomeAnalysisTK.jar -glm SNP -R test_human.fasta -T UnifiedGenotyper -I exome_recal_baq.bam -D 00-All.vcf -o exome_24apr_snp.vcf -metrics exome_24april_snp.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 -A DepthOfCoverage -A AlleleBalance

problem is that it does not report any SNP matching to dbsnp. All SNP,s are reported as novel. I am getting aroung 25000 SNPs and was wondering how can all these be novel.

I hope I am using right command and not missing something

Thanks,
Neha
neha is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:05 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO