I am trying to calculate the depth of coverage of an exome using gatk and am having trouble with two parts:
This is the command I am trying to emulate -
java -Xmx3072m -jar ./Sting/dist/GenomeAnalysisTK.jar \ -T DepthOfCoverage -I group1.READS.bam.list -L EXOME.interval_list \ -R ./human_g1k_v37.fasta \ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable \ --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 \ --includeRefNSites \ -o group1.DATA
first question is the group1.READS.bam.list I am confused by what they are asking for. Do they simply want paths to a handfulmy bam files separated by new lines?
second question is when I run the command it errors saying my contigs are incompatible.
Input files reads and reference have incompatible contigs: No overlapping contigs found. ERROR reads contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247... ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr20, chrY, chr19, chr22, chr21, chr6_ssto_hap7, chr6_mcf_hap5...
Is this an issue with the reference genome I used or my bam files? I used the hg19 because the human_g1k_v37 was erroring on the reference while hg19 did not.
Thank you enormously.