Haplotag command only tagging a small percentage of reads!

[DHmeduni]

Hi,
The phasing vcf looks good, but only a small percentage of reads are being haplotagged...I do have a deep coverage (>100x)
The same data with whatshap is able to phase and haplotag alot more.
the haplotag command for reference.

haplotag -b /data/test2/XXXXXXXX_bed.bam -s /data/test2/phased_prefix_SV.vcf -r /data/#references/chm13v2.0/chm13v2.0.fa --sv-file /data/test2/phased_prefix_SV.vcf -o /data/test2/haplotag --log -t 32

Any help would be must appreciated.
Thanks,
DH

[ythuang0522]

Hi @DHmeduni

From the command it looks like you provided the wrong SNP vcf file (phased_prefix_SV.vcf), assuming phased_prefix_SV.vcf only stores the phased SVs. We need both SNP and SV vcfs provided for haplotagging, because the number of SVs is way much less than SNPs. Can you check this first?

Yao-Ting

[DHmeduni]

I totally oversaw that!...WOW!