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Old 01-16-2012, 07:17 AM   #6
Jane M
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Location: Paris

Join Date: Aug 2011
Posts: 239
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Thanks for the answers.
I downloaded chr1.fa.gz from http://hgdownload.cse.ucsc.edu/golde...9/chromosomes/, I unzipped it. I tried to rerun both:

Quote:
java -Xmx2g -jar GenomeAnalysisTK.jar --refseq ~/chr1.fasta -T SomaticIndelDetector --minCoverage 10 -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
Quote:
java -Xmx2g -jar GenomeAnalysisTK.jar --refseq ~/chr1.fa -T SomaticIndelDetector --minCoverage 10 -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
but I still have the same error message... Isn't it suppose to work, even with a part of the genome?
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