Dear Dr. Wang,

SEQLinkage has great power compared with single variant linkage analysis. We plan to use it in WES data on 8 samples within a family.

The problem is that when we generate region markers, it shows the following error as "0 units detected".
But when we tried "--single-markers" analysis, every thing works fine.

Error when running regional markers:

seqlink --fam pedigree.fam --vcf chr22.vcf.gz -f MERLIN --recomb_cross_fam \

--build hg38
MESSAGE: Binary trait detected in [pedigree.fam]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 8 samples found in [chr22.vcf.gz]
MESSAGE: 1 families with a total of 8 samples will be scanned for 28,325 pre-defined units
MESSAGE: 0 units (from 0 variants) processed; 0 Mendelian inconsistencies and 0 recombination events handled
MESSAGE: 28,325 units ignored due to absence in VCF file
MESSAGE: Archiving regional marker data to directory [Linkage_Analysis/cache]
MESSAGE: 0 units will be converted to MERLIN format
MESSAGE: 0 units successfully converted to MERLIN format
MESSAGE: Archiving MERLIN format to directory [Linkage_Analysis/cache]
MESSAGE: Saving data to [Linkage_Analysis/LINKAGE]

Message when running single markers:
seqlink --fam pedigree.fam --vcf chr22.vcf.gz --freq EVSEAAF --single-markers \

--recomb_cross_fam --build hg38
-o LinkageAnalysisSNV -K 0.001 --moi AR -W 0 -M 1 --theta-max 0.5 --theta-inc 0.05 -j 8 --run-linkage
MESSAGE: Binary trait detected in [/pedigree.fam]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 8 samples found in [chr22.vcf.gz]

MESSAGE: 1 families with a total of 8 samples will be scanned for 41,131 pre-defined units
MESSAGE: 391 units processed {0.97%} ...

Thanks a lot and looking forward to your reply.

Stella Xia.