Can someone please help me with the following issue in the phase and impute step?
I am even having this issue while running the Glimpse tutorial. Any idea of what is going wrong here?
I run the following commands:
REF=reference_panel/split/1000GP.chr22.noNA12878 (this is the folder where there are bin files for each chromosome created in the split reference step?)
BAM=NA12878_1x_bam/NA12878.bam
while IFS="" read -r LINE || [ -n "$LINE" ];
do
printf -v ID "%02d" $(echo $LINE | cut -d" " -f1)
IRG=$(echo $LINE | cut -d" " -f3)
ORG=$(echo $LINE | cut -d" " -f4)
CHR=$(echo ${LINE} | cut -d" " -f2)
REGS=$(echo ${IRG} | cut -d":" -f 2 | cut -d"-" -f1)
REGE=$(echo ${IRG} | cut -d":" -f 2 | cut -d"-" -f2)
OUT=GLIMPSE_impute/NA12878_imputed
./bin/GLIMPSE2_phase --bam-file ${BAM} --reference ${REF}${CHR}${REGS}${REGE}.bin --output ${OUT}${CHR}${REGS}${REGE}.bcf
done < chunks.chr22.txt
__**Initialisation:
- Binary reference panel parsing ...
ERROR: Reading binary reference panel file:**__
Can someone please help me with the following issue in the phase and impute step?
I am even having this issue while running the Glimpse tutorial. Any idea of what is going wrong here?
I run the following commands:
REF=reference_panel/split/1000GP.chr22.noNA12878 (this is the folder where there are bin files for each chromosome created in the split reference step?)
BAM=NA12878_1x_bam/NA12878.bam
while IFS="" read -r LINE || [ -n "$LINE" ];
do
printf -v ID "%02d" $(echo $LINE | cut -d" " -f1)
IRG=$(echo $LINE | cut -d" " -f3)
ORG=$(echo $LINE | cut -d" " -f4)
CHR=$(echo ${LINE} | cut -d" " -f2)
REGS=$(echo ${IRG} | cut -d":" -f 2 | cut -d"-" -f1)
REGE=$(echo ${IRG} | cut -d":" -f 2 | cut -d"-" -f2)
OUT=GLIMPSE_impute/NA12878_imputed
./bin/GLIMPSE2_phase --bam-file ${BAM} --reference ${REF}${CHR}${REGS}${REGE}.bin --output ${OUT}${CHR}${REGS}${REGE}.bcf
done < chunks.chr22.txt
__**Initialisation:
ERROR: Reading binary reference panel file:**__