SHAPEIT phased haps file does not contain my SNPs of interest

Question

[michael.flower.14]

I produced a haps file using SHAPEIT, as below. However, when I query it to look for my 12 SNPs of interest, only 3 are in there. Does anyone know why? (PS they are not in the snp.strand.exclude file).

Thanks!

# Run a check to exclude erroring SNPs downstream
# With this first code chunk, an error is thrown but it generates the 'exclude' file
shapeit -check \
-P "$DIR"/plink/ped/$PREFIX"_chr4" \
-M "$MAP" \
--input-ref "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3_chr4.hap.gz "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3_chr4.legend.gz "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3.sample \
--output-log "$DIR"/shapeit/$PREFIX


# check is re-performed, but excluding the problematic variants (this runs to completion, without errors)
shapeit -check \
-P "$DIR"/plink/ped/$PREFIX"_chr4" \
-M "$MAP" \
--input-ref "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3_chr4.hap.gz "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3_chr4.legend.gz "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3.sample \
--exclude-snp "$DIR"/shapeit/$PREFIX".snp.strand.exclude"


# Phasing
shapeit -P "$DIR"/plink/ped/$PREFIX"_chr4" \
-M "$MAP" \
--input-ref "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3_chr4.hap.gz "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3_chr4.legend.gz "$EXT"/temp/map/1000GP_Phase3/1000GP_Phase3.sample \
--exclude-snp "$DIR"/shapeit/$PREFIX".snp.strand.exclude" \
-W 5 \
-O "$DIR"/shapeit/$PREFIX \
--states 200