Question: bwa mem + GATK +mutect
0
gravatar for naruto1nrt
3.2 years ago by
naruto1nrt20
Australia
naruto1nrt20 wrote:

align with bwa mem

realign and BQSR with GATK

then got the final bam

but when I use muTect to call somatic snv,I got an error.

 

command:

java -Xmx2g -jar muTect.jar \

       --analysis_type MuTect \

       --reference_sequence human_g1k_v37_decoy.fasta

       --cosmic b37_cosmic_v54_120711.vcf

       --dbsnp dbsnp_132_b37.leftAligned.vcf \

       --intervals region.bed \

       --input_file:normal N.bam \

       --input_file:tumor T.bam \

       --out  . \

       --coverage_file coverage.wig.txt

 

error:

##### ERROR ------------------------------------------------------------------------------------------

##### ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab): 

##### ERROR The invalid arguments or inputs must be corrected before the GATK can 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 allowable command-line arguments.

##### ERROR Visit our website and forum for extensive documentation and answers to 

##### ERROR commonly asked questions http://www.broadinstitute.org/gatk

##### ERROR

##### ERROR MESSAGE: SAM/BAM file T.bam is malformed: Error parsing SAM header. Problem parsing @PG key:value pair ID:139160T clashes with ID:bwa. Line:

##### ERROR @PG ID:bwa  PN:bwa  VN:0.7.8-r455   CL:bwa mem -t 8 -M -R @RG       ID:139160T      SM:139160T      LB:DHE00038     PU:DHE00038_L6  PL:illumina     CN:novogene human_g1k_v37_decoy.fasta T_1.clean.fq T_2.clean.fq; File T.bam; Line number 89

##### ERROR ------------------------------------------------------------------------------------------

 

should anyone offer a help to point why the error occured?

alignment software error • 3.2k views
ADD COMMENTlink modified 8 days ago by Biostar ♦♦ 20 • written 3.2 years ago by naruto1nrt20
0
gravatar for Pierre Lindenbaum
3.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum96k wrote:

I think that's a problem with the parsing of the BAM header. GATK tries to parse the @PG line but it also find a @RG tag. I would try to export the header of the BAM with "samtools view -H" in the @PG line remove everything after VN:0.7.8-r455 and use samtools reheader to insert the new header.

ADD COMMENTlink written 3.2 years ago by Pierre Lindenbaum96k
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