Combining VCF files using GATK?

[prs321]

Thank you, I will try it out. Appreciate it.

[lethalfang]

You may have mostly positions that are only called in one single replicates.

Try this as a test, just to extract only those positions that exist in all 5 replicates, to see if things are working as intended.

java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CombineVariants \
   -minN 5 \
   --variant rep1.vcf \
   --variant rep2.vcf \
   --variant rep3.vcf \
   --variant rep4.vcf \
   --variant rep5.vcf \
   -o combined.output.vcf

[prs321]

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT cs1 cs2 cs3 cs4 cs5
NODE_4_length_282_cov_38.510639 66 . G A 169.04 . AC=1;AF=0.500;AN=2;CIGAR=1X;DP=66;DPRA=0;GTI=0;LEN=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;TYPE=snp;set=Intersection GT:AOP:PL:QA:QR:RO 0/1:9:19:100,0
,100:271:306:10 . . . .
NODE_4_length_282_cov_38.510639 99 . C T 214.21 . AC=1;AF=0.500;AN=2;CIGAR=1X;DP=92;DPRA=0;GTI=0;LEN=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;TYPE=snp;set=Intersection GT:AOP:PL:QA:QR:RO 0/1:12:24:100,
0,100:319:364:11 . . . .
NODE_4_length_282_cov_38.510639 114 . A G 346.87 . AC=1;AF=0.500;AN=2;CIGAR=1X;DP=102;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;TYPE=snp;set=Intersection GT:AOP:PL:QA:QR:RO 0/1:14
:26:100,0,100:475:413:12 . . . .
NODE_4_length_282_cov_38.510639 154 . G A 452.29 . AC=1;AF=0.500;AN=2;CIGAR=1X;DP=123;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;TYPE=snp;set=Intersection GT:AOP:PL:QA:QR:RO 0/1:18
:31:100,0,100:578:467:13 . . . .
NODE_4_length_282_cov_38.510639 247 . T G 355.03 . AC=1;AF=0.500;AN=2;CIGAR=1X;DP=131;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;TYPE=snp;set=Intersection GT:AOP:PL:QA:QR:RO
0/1:14:32:100,0,100:484:576:18 . . . .
NODE_9_length_16257_cov_15.910501 5514 . C A 248.89 . AB=0;ABP=0;AC=2;AF=1.00;AN=2;CIGAR=1X;DP=68;DPRA=0;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QR=0;RO=0;RPPR=0;RUN=1;SRF=0;SR
P=0;SRR=0;TYPE=snp;set=Intersection GT:AOP:PL:QA:QR:RO 1/1:11:11:100,33,0:341:0:0 . . . .
NODE_9_length_16257_cov_15.910501 9753 . T G 0 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;CIGAR=1X;DP=45;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;SAR=0;TYPE=snp;set=cs1-cs4
GT:AOP:PL:QA:QR:RO 0/0:6:28:7,0,100:39:587:22 . . . .
NODE_9_length_16257_cov_15.910501 12869 . T G 0 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;CIGAR=1X;DP=85;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;TYPE=snp;set=cs1-cs2-cs3 GT:AO:
DP:PL:QA:QR:RO 0/0:8:28:34,0,100:59:485:20 . . . .
NODE_9_length_16257_cov_15.910501 14192 . T G 0 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;CIGAR=1X;DP=37;DPRA=0;GTI=0;LEN=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;SAR=0;TYPE=snp;set=cs2-cs4 GT:AOP:PL:QA
:QR:RO . 0/0:4:19:1,0,100:24:385:15 . . .
NODE_9_length_16257_cov_15.910501 14201 . A G 0 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;CIGAR=1X;DP=33;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;SAR=0;TYPE=snp;set=cs2-cs3
GT:AOP:PL:QA:QR:RO . 0/0:4:17:5,0,100:24:385:13 . . .
NODE_9_length_16257_cov_15.910501 14240 . T G 0 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;AO=4;CIGAR=1X;DP=36;DPB=18;DPRA=0;EPP=11.6962;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;
RO=14;RPP=11.6962;RUN=1;SAF=4;SAP=11.6962;SAR=0;TYPE=snp;set=cs2-cs4 GT:AOP:PL:QA:QR:RO . 0/0:4:18:3,0,100:24:383:14 . . .
NODE_9_length_16257_cov_15.910501 14261 . T G 0 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;CIGAR=1X;DP=36;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;RUN=1;SAR=1;TYPE=snp;set=cs1-cs
3 GT:AOP:PL:QA:QR:RO 0/0:6:21:24,0,100:44:299:15 . . . .
NODE_9_length_16257_cov_15.910501 14263 . A G 0.01 . AB=0;ABP=0;AC=0;AF=0.00;AN=2;CIGAR=1X;DP=27;DPRA=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;RUN=1;SAF=1;TYPE=snp;set=cs3-cs4
GT:AOP:PL:QA:QR:RO . . 0/0:5:15:22,0,61:35:78:10 . .

[lethalfang]

There are actually 5 columns, but only the first column is listed with the genotype. The other 4 have a '.' under them.

Can you show me a few rows of the output?

[prs321]

There are actually 5 columns, but only the first column is listed with the genotype. The other 4 have a '.' under them.

[lethalfang]

There is only one such column? If you combine 5 samples (replicates), there should be 5 such columns.
If not, make sure the header for the sample info are different in each of the 5 vcf files. Otherwise GATK thinks it's the same sample (i.e., same replicate in this case).
0/0 means reference calls in both copies.

[prs321]

0/0:6:21:24,0,100:44:299:15 . . . .

[lethalfang]

Yes so for example I have 5 alignment files: rep1.bam, rep2.bam, rep3.bam, rep4.bam, rep5.bam

All of them have been processed (markduplicates, addreadgroups etc).

Then I called snps on each alignment to produce the following: rep1.vcf, rep2.vcf, rep3.vcf, rep4.vcf, rep5.vcf

What will this give you?

java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CombineVariants \
   -minN 2 \
   --variant rep1.vcf \
   --variant rep2.vcf \
   --variant rep3.vcf \
   --variant rep4.vcf \
   --variant rep5.vcf \
   -o combined.output.vcf

[prs321]

Yes so for example I have 5 alignment files: rep1.bam, rep2.bam, rep3.bam, rep4.bam, rep5.bam

All of them have been processed (markduplicates, addreadgroups etc).

Then I called snps on each alignment to produce the following: rep1.vcf, rep2.vcf, rep3.vcf, rep4.vcf, rep5.vcf

[lethalfang]

The issue seems to be that when I combine all 5 vcf files for the replicates, it shows a replicate at 1 site, but shows a '.' for the other 4.

I'm not really sure how to go about this.

Does that mean only 1 replicate has that called variant?

[prs321]

The issue seems to be that when I combine all 5 vcf files for the replicates, it shows a replicate at 1 site, but shows a '.' for the other 4.

I'm not really sure how to go about this.

[lethalfang]

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants.html

If you want to only show variants in 2+ duplicates, use "--minimumN 2" option.

[prs321]

Here is my task. I have 4 treatment groups containing 5 replicates in each group.

For each treatment group, I am looking for at least 2 replicates that have the same base substitution.

So far I have generated a vcf file for each replicate in each treatment group.

1. What is the best way to combined these files so that I have 4 vcf files, 1 for each treatment group that contains 5 replicates?

2. What is the best way to keep track of the position of sites where at least 2 replicates showed the same base substitution so that I can produce results once the gene annotation is complete?