Why are the results of all samples like this: ploidy=2.00; purity=NA?

[h170607]

cnv_facets.R -T $bed --gbuild hg19 -t $tumor -n $normal -vcf $dbsnp -o ${sample}

The dbSNP file was downloaded from https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz. Then the file was processed to add "chr" using bcftools annotate and tabix.

Warning message: In max(mafR.clust[seg$chrom < nX & seg$nhet > min.nhet], na.rm = T) : max里所有的参数都不存在；回覆-Inf

[dariober]

I think https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz is relative to hg38 but you specify --gbuild hg19.

I don't know if this is the cause of the warning but I would first make sure that your bam, vcf, and --gbuild are consistent with each other. This post https://www.biostars.org/p/396813/ has some discussion about getting dbSNP for hg19 if that's what you need.