Problems runnig WES, weird segmentation?

Hi there,

I have several WES cfDNA samples at ~90X of coverage and am getting some strange final ichorCNA results: it seems like the "binning" or something related to the coverage isn't working well.

Could you please help me to identify what I'm missing? This is the code I run:

$ readCounter --window 1000000 --quality 20 \
    --chromosome "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" \
    bamfile > bamfile.wig

$ Rscript runIchorCNA.R \
    --gcWig gc_hg38_1000kb.wig --mapWig map_hg38_1000kb.wig \
    --centromere GRCh38.GCA_000001405.2_centromere_acen.txt \
    --normalPanel HD_ULP_PoN_hg38_1Mb_median_normAutosome_median.rds \
    --exons.bed xgen-exome-hyb-panel-v2-probes-hg38.bed \
    --plotYLim "c(-1,1)" \
    --id bamfile_name --WIG bamfile.wig \
    --ploidy "c(2)" --maxCN 5 --normal "c(0.5,0.6,0.7,0.8,0.9,0.95,0.99)" \
    --includeHOMD False --estimateNormal True --estimatePloidy True \
    --genomeBuild "hg38" --genomeStyle "UCSC" --chrs "c(1:22)" --chrTrain "c(1:22)" \
    --estimateScPrevalence False --scStates "c(1,3)"

Thanks

broadinstitute / ichorCNA

Problems runnig WES, weird segmentation? #138