zhenxian
Hi, Yes, the `r941_prom_hac_g360+g422` model is recommended for Guppy3 and Guppy4 data.
@bcantarel Great thanks for your suggestions! We added some fields to output the normal sample information, including normal depth and alternate count in normal BAM: ``` ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT=...
Yes, we combined the tumor and normal tags into `FORMAT` column, here are some lines for reference: ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE chr17 80000548...
@hillstub Could you pls check if the site 984 was found in the `pileup.vcf.gz`?
Hi, @mproberts99, Thanks for the log. Seem all low-coverage variants were reported by the full-alignment model. We will check and get back to you soon.
@lagphase By default, Clair3 would discard all supplementary alignments. So you might disable the supplementary alignments in IGV to see if the variant is evident.
@sachiwije Please follow the [instructions](https://github.com/HKU-BAL/Clair3/issues/149#issuecomment-1319644808) to install Clair3 in MacOS.
Value Error: A BGZF (e.g. a BAM file) block should start with b'\x1f\x8b\x08\x04', not b'\xf12\xdeB'
Hi, @husamia, It seems either BAM or the reference file is a corrupted BGZF file. Could you try to decompress the BAM and reference file and re-index them to see...
@ASLeonard Billion thanks for the PR! Will test then.
Hi, @gtollefson, The './.' variants indicate low-AF sites that were not processed by Clair3 and thus not subsequently included in the output. To output these variants as `RefCall`, you can...