search

Personalis-DASH / DASH

Other
9 stars 2 forks source link

how to get the input parameters "--normal_read_count" and "--tumor_read_count" #5

Open rubickkkkk opened 1 year ago

rubickkkkk commented 1 year ago

I used the code "echo $(cat "HLA_reads.normal.fasta"|wc -l)/4|bc" to calculated the reads in your example fastq. but I only got the 125000 which is inconsistent with the parameters you provided "166545259.1184". how can I get this parameter from either fastq or bam, and Why does your input parameter contain a decimal point?

looking forward for your replies.

Personalis-DASH commented 11 months ago

Hello, great question. I have no idea how the decimals got in there and have no removed them. Your read counts should indeed be integers. I've provided small sample fastq files that only contain HLA relevant reads. The 'normal_read_count' and 'tumor_read_count' parameters are in reference to the full fastqs. I haven't included that data in the github, so it can't be calculated here; however, you can use your same command on your full fastq files and it should work!