Reference genome with the prefix 'chr'

[joonlee3]

Gavin,

I took a look at some of the data sets in ichorCNA and found out that chromosome names are numeric (without the prefix 'chr') I am wondering if ichorCNA can deal with bam generated with hg19 with the prefix 'chr'

Please let me know.

Thanks, Joon

[jurhoades]

Hi Joon,

You should be able to use BAM files with or without the "chr" contig prefix (see https://github.com/broadinstitute/ichorCNA/commit/88e541d07f45bfa96a3cab5a584d5bc5b6ae8ac3) . ichorCNA uses GenomeInfoDb R package to properly read common contig formats. Let us know if you run into any trouble.

[joonlee3]

Thanks,

As you suggested, I ran ichorCNA with the normal panel data provided in the 'extdata' by the 'ichorCNA' package. I've got the following error:

Parsing: fixedStep chrom=1 start=1 step=500000 span=500000 Parsing: fixedStep chrom=2 start=1 step=500000 span=500000 Parsing: fixedStep chrom=3 start=1 step=500000 span=500000 Parsing: fixedStep chrom=4 start=1 step=500000 span=500000 Parsing: fixedStep chrom=5 start=1 step=500000 span=500000 Parsing: fixedStep chrom=6 start=1 step=500000 span=500000 Parsing: fixedStep chrom=7 start=1 step=500000 span=500000 Parsing: fixedStep chrom=8 start=1 step=500000 span=500000 Parsing: fixedStep chrom=9 start=1 step=500000 span=500000 Parsing: fixedStep chrom=10 start=1 step=500000 span=500000 Parsing: fixedStep chrom=11 start=1 step=500000 span=500000 Parsing: fixedStep chrom=12 start=1 step=500000 span=500000 Parsing: fixedStep chrom=13 start=1 step=500000 span=500000 Parsing: fixedStep chrom=14 start=1 step=500000 span=500000 Parsing: fixedStep chrom=15 start=1 step=500000 span=500000 Parsing: fixedStep chrom=16 start=1 step=500000 span=500000 Parsing: fixedStep chrom=17 start=1 step=500000 span=500000 Parsing: fixedStep chrom=18 start=1 step=500000 span=500000 Parsing: fixedStep chrom=19 start=1 step=500000 span=500000 Parsing: fixedStep chrom=20 start=1 step=500000 span=500000 Parsing: fixedStep chrom=21 start=1 step=500000 span=500000 Parsing: fixedStep chrom=22 start=1 step=500000 span=500000 Parsing: fixedStep chrom=X start=1 step=500000 span=500000 Parsing: fixedStep chrom=Y start=1 step=500000 span=500000 Sorting by decreasing chromosome size Correcting Tumour Loading required package: GenomeInfoDb Removed 163 bins near centromeres. Applying filter on data... Correcting for GC bias... Correcting for mappability bias... Filtering low uniqueness regions with mappability score < 0.9 Determining gender...Gender unknown Error in [[<-(*tmp*, name, value = c(NA, -0.0448071293651577, NA, : 5229 elements in value to replace 4987 elements Calls: normalizeByPanelOrMatchedNormal -> $<- -> $<- -> [[<- -> [[<- In addition: Warning messages: 1: In tumour_copy$copy - panel$Median : longer object length is not a multiple of shorter object length Execution halted

FYI:

• Instead of using the normal panel data, I launched a test run with a pseudo-matched normal Wig. It worked well.

Best, Joon