Hello,
I am using GATK for the first time. I try to use SomaticIndelDetectorWalker. I have difficulties with the option -R ref.fasta.
I read:
From this, I understand that this option is not mandatory. When I try:
I have the error:
It seems that I should provide a reference fasta file. Then, I tried:
but I have this error:
I think the problem is my fasta file. The one that I provide contains only:
Could someone explains me what is this refseq.fasta file precisely?
Thanks for any help
I am using GATK for the first time. I try to use SomaticIndelDetectorWalker. I have difficulties with the option -R ref.fasta.
I read:
--refseq String NA Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name
java -Xmx2g -jar GenomeAnalysisTK.jar -T SomaticIndelDetector -o indels.vcf -verbose indels.txt -I:normal ../../../../data/patient1/s_garma-fibros_converted.bam -I:tumor ../../../../data/patient1/s_garma-296_converted_sorted.bam
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-15-gcd43f01):
##### 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 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: Walker requires a reference but none was provided.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-15-gcd43f01):
##### 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 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: Walker requires a reference but none was provided.
##### ERROR ------------------------------------------------------------------------------------------
java -Xmx2g -jar GenomeAnalysisTK.jar -R ~/hg19.fasta -T SomaticIndelDetector -o indels.vcf -verbose indels.txt -I:normal ../../../../data/patient1/s_garma-fibros_converted.bam -I:tumor ../../../../data/patient1/s_garma-296_converted_sorted.bam
##### ERROR A USER ERROR has occurred (version 1.4-15-gcd43f01):
##### 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 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: Invalid command line: Failed to load reference dictionary
##### 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 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: Invalid command line: Failed to load reference dictionary
Code:
chr1 249250621 6 50 51 chr2 243199373 254235646 50 51 chr3 198022430 502299013 50 51 chr4 191154276 704281898 50 51 chr5 180915260 899259266 50 51 chr6 171115067 1083792838 50 51 chr7 159138663 1258330213 50 51 chr8 146364022 1420651656 50 51 chr9 141213431 1569942965 50 51 chr10 135534747 1713980672 50 51 chr11 135006516 1852226121 50 51 chr12 133851895 1989932775 50 51 chr13 115169878 2126461715 50 51 chr14 107349540 2243934998 50 51 chr15 102531392 2353431536 50 51 chr16 90354753 2458013563 50 51 chr17 81195210 2550175419 50 51 chr18 78077248 2632994541 50 51 chr19 59128983 2712633341 50 51 chr20 63025520 2772944911 50 51 chr21 48129895 2837230949 50 51 chr22 51304566 2886323449 50 51 chrX 155270560 2938654113 50 51 chrY 59373566 3097030091 50 51 chrMt 16571 3157591135 50 51
Thanks for any help
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