Interpreting results

[MaryGoAround]

Hi

I could run PureCN on one cell line (tumour)

for BAM in $TUMOR_BAMS; do
    SAMPLE_ID=$(basename $BAM .bam)
    VCF_PATH="tumor.vcf.gz"
    Rscript $PURECN/PureCN.R --out output \
        --tumor coverage_loess.txt.gz \
        --sampleid $SAMPLE_ID --vcf $VCF_PATH --normaldb normalDB_wgs_hg38.rds \
        --intervals baits_hg38_intervals.txt --genome hg38 \
        --mapping-bias-file mapping_bias_wgs_hg38.rds \
        --fun-segmentation PSCBS --force --post-optimize --seed 123 --max-copy-number 8 --min-purity 0.9 --max-purity 0.99 \
        --model-homozygous TRUE

I got this plots

Am I right there is some loss in chr8 and some gain chr16?

Please correct me if I interpret the plot correctly

Gray dots: Represent individual copy number bins for segments across the genome. These points reflect raw copy number values. Purple and Red Lines: Indicate the segmented copy number. The two lines represent the major allele (C1) and minor allele (C2). Purple Line: Major allele (C1) Red Line: Minor allele (C2)

Thanks for any thoughts