holtjma
commented
3 months ago Hello,
HiPhase looks for the sample name in the VCF and the BAM file to match. It sounds like you know they mismatch, so I would recommend making them match and retrying it.
Matt
root@3ca21770deb6:/sequencing/Deepvariant# hiphase --reference pbr.v1.1.chr.fasta --bam Whangkeumbae_sorted.bam --vcf whangk uembae.vcf.gz --output-vcf whangkeumbae.phased.vcf [2024-05-27T01:41:46.671Z INFO hiphase::cli] Alignment file: "Whangkeumbae_sorted.bam" [2024-05-27T01:41:46.671Z INFO hiphase::cli] Variant file: "whangkuembae.vcf.gz" [2024-05-27T01:41:46.671Z INFO hiphase::cli] Reference file: "pbr.v1.1.chr.fasta" [2024-05-27T01:41:46.671Z INFO hiphase::cli] Minimum call quality: 0 [2024-05-27T01:41:46.671Z INFO hiphase::cli] Minimum mapping quality: 5 [2024-05-27T01:41:46.671Z INFO hiphase::cli] Minimum matched alleles: 2 [2024-05-27T01:41:46.671Z INFO hiphase::cli] Minimum spanning reads: 1 [2024-05-27T01:41:46.671Z INFO hiphase::cli] Supplemental mapping block joins: ENABLED [2024-05-27T01:41:46.671Z INFO hiphase::cli] Phase singleton blocks: DISABLED [2024-05-27T01:41:46.671Z INFO hiphase::cli] Local re-alignment maximum reference buffer: +-15 bp [2024-05-27T01:41:46.671Z INFO hiphase::cli] Global re-alignment: DISABLED [2024-05-27T01:41:46.671Z INFO hiphase::cli] Processing threads: 1 [2024-05-27T01:41:46.671Z INFO hiphase::cli] I/O threads: 1 [2024-05-27T01:41:46.697Z ERROR hiphase] User provided 1 BAM files, but only 0 matched samples for phasing [2024-05-27T01:41:46.697Z ERROR hiphase] Please remove extra BAM files or add additional samples, BAMs matching phasing: []
I think I have an issue with my input file. Is this a matter of 'sample name' on BAM file? (aligned bamfile @RG header)
Input BAM file has unnamed samplename, while VCF file has specific sample name (ex, Asian pear)
Should I add a sample name on BAM file to solve the error?
Thanks