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(Quote) hi Geraldine, i have the target region coordiate information like this:chr1 10137431 10137716; With this guide https://www.broadinstitute.org/gatk/guide/article?id=1329 i have got the refseq fiile. chr1 2323213 2336885 NM_00703…
@Sheila If i use the same file to calling variants by HaplotypeCaller. Everything looks like fine. but once i run BaseRecalibrator, the erorr will happened.
@Sheila Thanks Sheila, Yes, i have filter low quality reads by our programme before analysis. So how to solve this problem? Many thanks.
@Geraldine_VdAuwera Hi Geraldine, When i run BaseRecalibrator: /home/elvis/software/JAVA/jre1.7.0_67/bin/java -Xmx15g -jar /home/elvis/software/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -R /home/george/hg19/ucsc.hg19.fa…
(Quote) Hi Geraldine_VdAuwera java -jar /usr/local/software/picard-tools-1.105/ReorderSam.jar I=./aCGH5875.sam O=./Reorder.sam REFERENCE=/home/george/alignment/gatk_resource/ucsc.hg19.fasta After aln the fasta file, in reorder process I also confr…
(Quote) Hi, you meaning this ft: ftp://ftp.broadinstitute.org/bundle/2.8/b37/ but in here, i didn't find any b37 genomic reference.