VisCap

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Hello, thanks for letting your project open. I'm trying to test it and I'm facing this warnings:

Warning messages:
1: In image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks,  :
  unsorted 'breaks' will be sorted before use
2: In matrix(ncol = 2, byrow = TRUE, data = c("Date", date(), "VisCap command",  :
  data length [35] is not a sub-multiple or multiple of the number of rows [18]

I don't understand this sentences, it can cause some error in my results?

Cheers, George Carvalho

Hi George, did you follow the instructions on preparing you interval file? Can you send me a few lines of you interval file you are using? And, how do you get the depth of coverage files?

Yes, my first bed file:

chr16	68771313	68771371	CDH1__NM_004360__exon__1__chr16__f	0	+
chr16	68772194	68772319	CDH1__NM_004360__exon__2__chr16__f	0	+
chr16	68835567	68835801	CDH1__NM_004360__exon__3__chr16__f	0	+
chr16	68842321	68842475	CDH1__NM_004360__exon__4__chr16__f	0	+
chr16	68842590	68842756	CDH1__NM_004360__exon__5__chr16__f	0	+
chr16	68844094	68844249	CDH1__NM_004360__exon__6__chr16__f	0	+
chr16	68845581	68845767	CDH1__NM_004360__exon__7__chr16__f	0	+
chr16	68846032	68846171	CDH1__NM_004360__exon__8__chr16__f	0	+
chr16	68847210	68847403	CDH1__NM_004360__exon__9__chr16__f	0	+
chr16	68849412	68849667	CDH1__NM_004360__exon__10__chr16__f	0	+
...

My second bed file:

#chrom	start	end	interval_name
chr16	68771313	68771371	CDH1,NM_004360,exon,1,chr16,f
chr16	68772194	68772319	CDH1,NM_004360,exon,2,chr16,f
chr16	68835567	68835801	CDH1,NM_004360,exon,3,chr16,f
chr16	68842321	68842475	CDH1,NM_004360,exon,4,chr16,f
chr16	68842590	68842756	CDH1,NM_004360,exon,5,chr16,f
chr16	68844094	68844249	CDH1,NM_004360,exon,6,chr16,f
chr16	68845581	68845767	CDH1,NM_004360,exon,7,chr16,f
chr16	68846032	68846171	CDH1,NM_004360,exon,8,chr16,f
chr16	68847210	68847403	CDH1,NM_004360,exon,9,chr16,f
...

With both I had the same warning. About the GATK (3.6-0-g89b7209) DepthOfCoverage command:

$ gatk -T DepthOfCoverage -R /path/to/ucsc.hg19.fa -o sample1  -I /path/to/sample1.bam -L /path/to/intervals.bed

Thanks!

Hi George, both of the bed files seem to be correctly formatted. Make sure you are using the same bed file for running the DofCove tool. If you are doing so, and still getting the error, please send me a sample of your depthofcoverage output, your bed file, your config file and your command line for running VisCap. Thank you, Arna

Hi George,

Just following up with you if your problem with VisCap persists. Please let me know and send me your input so that I can examine the issue. Thanks! Arna