@vplagnol
Hi. I am facing the error in countBamInGRanges. I tried with many of my bam files (hg19) and the bam which was provided in the ExomeDepth's github page also but still I'm not able to rectify the error.
Reference fasta file provided so ExomeDepth will compute the GC content in each window
Parse 1 BAM files
[1] "new.bam"
Now parsing new.bam
Error in countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, :
Some sequences in the target data frame cannot be found in the index of the BAM file
In addition: Warning messages:
1: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, :
Problematic sequences:
2: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, :
12345678910111213141516171819202122XYMTGL000207.1GL000226.1GL000229.1GL000231.1GL000210.1GL000239.1GL000235.1GL000201.1GL000247.1GL000245.1GL000197.1GL000203.1GL000246.1GL000249.1GL000196.1GL000248.1GL000244.1GL000238.1GL000202.1GL000234.1GL000232.1GL000206.1GL000240.1GL000236.1GL000241.1GL000243.1GL000242.1GL000230.1GL000237.1GL000233.1GL000204.1GL000198.1GL000208.1GL000191.1GL000227.1GL000228.1GL000214.1GL000221.1GL000209.1GL000218.1GL000220.1GL000213.1GL000211.1GL000199.1GL000217.1GL000216.1GL000215.1GL000205.1GL000219.1GL000224.1GL000223.1GL000195.1GL000212.1GL000222.1GL000200.1GL000193.1GL000194.1GL000225.1GL000192.1NC_007605hs37d5
3: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, :
chr1chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr2chr20chr21chr22chr3chr4chr5chr6chr7chr8chr9
@vplagnol Hi. I am facing the error in countBamInGRanges. I tried with many of my bam files (hg19) and the bam which was provided in the ExomeDepth's github page also but still I'm not able to rectify the error. Reference fasta file provided so ExomeDepth will compute the GC content in each window Parse 1 BAM files [1] "new.bam" Now parsing new.bam Error in countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, : Some sequences in the target data frame cannot be found in the index of the BAM file In addition: Warning messages: 1: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, : Problematic sequences: 2: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, : 12345678910111213141516171819202122XYMTGL000207.1GL000226.1GL000229.1GL000231.1GL000210.1GL000239.1GL000235.1GL000201.1GL000247.1GL000245.1GL000197.1GL000203.1GL000246.1GL000249.1GL000196.1GL000248.1GL000244.1GL000238.1GL000202.1GL000234.1GL000232.1GL000206.1GL000240.1GL000236.1GL000241.1GL000243.1GL000242.1GL000230.1GL000237.1GL000233.1GL000204.1GL000198.1GL000208.1GL000191.1GL000227.1GL000228.1GL000214.1GL000221.1GL000209.1GL000218.1GL000220.1GL000213.1GL000211.1GL000199.1GL000217.1GL000216.1GL000215.1GL000205.1GL000219.1GL000224.1GL000223.1GL000195.1GL000212.1GL000222.1GL000200.1GL000193.1GL000194.1GL000225.1GL000192.1NC_007605hs37d5 3: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, : chr1chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr2chr20chr21chr22chr3chr4chr5chr6chr7chr8chr9