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PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
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About haplotype output #64

Closed woshiakai5525 closed 1 year ago

woshiakai5525 commented 1 year ago

pb-CpG-tools is a powerful and useful tool to me. But I can't output hap.bed and hap.bw files. I will show you my command line as below.

aligned_bam_to_cpg_scores --bam haplotagged.bam --model pileup_calling_model.v1.tflite --output-prefix cpg_output --threads 24 --hap-tag HP

The haplotagged.bam is phased by whatshap, and I have confirmed the hap tag in the bam file as "HP:i:1" or "HP:i:2". The output files are only cpg_output.combined.bed and cpg_output.combined.bw but hap1 and hap2 files. The version is aligned_bam_to_cpg_scores 2.3.1.

Could you correct my mistake or give me some advice? Thank you.

ctsa commented 1 year ago

Thanks, this is unexpected, especially since whatshap output is tested.

  1. Does aligned_bam_to_cpg_scores complete and exit 0 when this happens?
  2. Do the combined bed/bw tracks contain the information you expect?
  3. Can you share a few SAM lines of the bam input as examples?
woshiakai5525 commented 1 year ago

Thanks, this is unexpected, especially since whatshap output is tested.

  1. Does aligned_bam_to_cpg_scores complete and exit 0 when this happens?
  2. Do the combined bed/bw tracks contain the information you expect?
  3. Can you share a few SAM lines of the bam input as examples?

Thank you for your quick response. I am sorry I made a mistake in my bam file. I have already corrected my mistake and outputted the hap1 and hap2 bw/bed files. Sorry for the inconvenience and please close this issue.

ctsa commented 1 year ago

No problem, good to hear things are working.