PureCN: Estimating tumor purity and ploidy

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5.7 years ago

sruthi ▴ 40

Hi, I tried calculating GC normalized coverage by giving .bam file and intervals.txt file as input and the following error showed up. I tried viewing the BAM file for the error, but file size being big, it ain't happening. What should I do to troubleshoot the error?

Error in .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file), : seqlevels(param) not in BAM header: seqlevels: ‘chrY’ file: /path/to/sample.bam index: /path/to/sample.bam

TIA

next-gen sequencing • 1.5k views

ADD COMMENT • link 5.7 years ago by sruthi ▴ 40

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Are the BAM files aligned to the same FASTA file that was used to generate the interval file?

ADD REPLY • link 5.7 years ago by markus.riester ▴ 550

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No. I will align the BAM file again and then run the tool.

Thanks Markus

ADD REPLY • link 5.7 years ago by sruthi ▴ 40

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Hey, I would also like to know whether IDT xgen provides hg38.bed file. While looking for .bed files on their website, I could find only the one for hg19 and not hg38. Could you please give me a clarity on this?