X chromosome

[KatieSaxby46]

As my data includes the X chromosome I needed to comment out line 3 below and remove the # from line 2.

echo "Analysing the phenotype ${PHENOTYPE}."
# for CHR in $(seq 1 22) X; do
for CHR in $(seq 1 22); do

Could this part of analyser.sh become automated, so if 'data....chrX' exists then for CHR in $(seq 1 22) X; do
I also didn't initially realise that I needed to specify IMPUTEDDATA_CHRX, OR SAMPLEFILE_CHR_X