0 units (from 0 variants) processed; 28,325 units ignored due to absence in VCF file

[StellaXia]

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.

[StellaXia]

I checked the difference between our vcf with the example vcf file in github.
Will this error be due the missing of SNP ID in our vcf file?

Our vcf file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
chr22 10526438 . A G 85.1 . AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=3;MLEAF=1;MQ=50.99;QD=31.18;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS ./.:2,0:2:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. 1|1:0,2:2:6:1|1:10526438_A_G:90,6,0:10526438 ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:.
chr22 10526445 . A G 85.1 . AC=2;AF=1;AN=2;DP=4;ExcessHet=3.0103;FS=0;MLEAC=3;MLEAF=1;MQ=50.99;QD=29.28;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS ./.:2,0:2:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. 1|1:0,2:2:6:1|1:10526438_A_G:90,6,0:10526438 ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:. ./.:0,0:0:.:.:.:0,0,0:.
chr22 10527034 . G T 44.1 . AC=2;AF=1;AN=2;DP=2;ExcessHet=3.0103;FS=0;MLEAC=3;MLEAF=1;MQ=60;QD=22.05;SOR=0.693 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 1/1:0,2:2:6:49,6,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0
chr22 10534861 . T G 75.56 . AC=2;AF=1;AN=2;DP=3;ExcessHet=3.0103;FS=0;MLEAC=3;MLEAF=1;MQ=41.42;QD=25.19;SOR=1.179 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 1/1:0,3:3:9:81,9,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0
chr22 10536709 . T C 75.56 . AC=2;AF=1;AN=2;DP=3;ExcessHet=3.0103;FS=0;MLEAC=3;MLEAF=1;MQ=39.59;QD=25.19;SOR=1.179 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 1/1:0,3:3:9:81,9,0

Thanks!