MuTect contig error..

[shyam_la]

I am entirely new to NextGen Sequencing data analysis and have been working on a project for a week. We have whole human exome 100bp paired end data from an Illumina HiSeq system, we are working on. Base calls are of good quality as assessed by FastQC.

I am using all open source software.

Raw reads - Index reference genome with BWA - Align with BWA - sampe with BWA adding RG line - SAM to BAM with samtools - Mark and remove PCR duplicates with Picard - RealignerTargetCreator and IndelRealigner using knowns 1000G and Mills n 1000G with GATK - FixMateInformation with Picard - Count covariates using dbSNP135 and base quality score recalibration with GATK. All with default parameters.

Just ran MuTect (beta) and got this error:

E:\Exome>java -Xmx1g -jar MuTect\mutect.jar --analysis_type MuTect --reference_s
equence UCSChg19\ucsc.hg19.fasta -B:cosmic,VCF Mutect\hg19_cosmic.vcf -B:dbsnp,V
CF ucschg19\dbsnp_135.hg19.vcf --input_file:normal P01_normal_ready.bam --input_
file:tumor P01_cancer_ready.bam --out call_stats.out --coverage_file coverage.wi
g.txt
INFO 10:38:26,672 HelpFormatter - ---------------------------------------------
------------------------------------
INFO 10:38:26,682 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.1-37-g5
cedb2d, Compiled 2011/09/14 10:01:32
INFO 10:38:26,683 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:38:26,683 HelpFormatter - Please view our documentation at http://www.b
roadinstitute.org/gsa/wiki
INFO 10:38:26,683 HelpFormatter - For support, please view our support site at

http://getsatisfaction.com/gsa

INFO 10:38:26,684 HelpFormatter - Program Args: --analysis_type MuTect --refere
nce_sequence UCSChg19\ucsc.hg19.fasta -B:cosmic,VCF Mutect\hg19_cosmic.vcf -B:db
snp,VCF ucschg19\dbsnp_135.hg19.vcf --input_file:normal P01_normal_ready.bam --i
nput_file:tumor P01_cancer_ready.bam --out call_stats.out --coverage_file covera
ge.wig.txt
INFO 10:38:26,684 HelpFormatter - Date/Time: 2012/06/06 10:38:26
INFO 10:38:26,684 HelpFormatter - ---------------------------------------------
------------------------------------
INFO 10:38:26,686 HelpFormatter - ---------------------------------------------
------------------------------------
INFO 10:38:26,707 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:38:27,308 RMDTrackBuilder - Loading Tribble index from disk for file Mu
tect\hg19_cosmic.vcf
INFO 10:38:27,862 RMDTrackBuilder - Loading Tribble index from disk for file uc
schg19\dbsnp_135.hg19.vcf
##### ERROR --------------------------------------------------------------------
----------------------
##### ERROR A USER ERROR has occurred (version 1.1-37-g5cedb2d):
##### ERROR The invalid arguments or inputs must be corrected before the GATK ca
n proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowabl
e command-line arguments.
##### 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://g
etsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Input files cosmic and reference have incompatible contigs:
No overlapping contigs found.
##### ERROR cosmic contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 1
5, 16, 17, 18, 19, 20, 21, 22]
##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr
7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, ch
r19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random
, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr
6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ss
to_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_
gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_rando
m, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204
_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, ch
r19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl00021
1, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl00021
6, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl00022
1, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl00022
6, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl00023
1, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl00023
6, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl00024
1, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl00024
6, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR --------------------------------------------------------------------
----------------------

Any easy solutions?

[ron128]

What reference files are you using? There looks to be some sort of disparity between your reference files

[shyam_la]

What reference files are you using? There looks to be some sort of disparity between your reference files

This issue is long resolved now!! Thanks!

[ron128]

oh k! glad for that. I thought as much so seeing as to how old this query is just chanced upon this while looking up mutect on board..

If its not too much of a bother do you mind posting how you solved it? Was it because of the different reference genomes used? Just for documentation of error.

[shyam_la]

The .fasta file I was using had contigs chr1, chr2, chr3 and so on.. I just got hold of another fasta file that has contigs 1, 2 .. X, Y, M and used the latter.
That resolved the issue, as Mutect's cosmic file uses this naming convention..