When pivoting and including metadata columns, if metadata columns are different for some samples for the same variant, they will be reported separately.
CHROM
POS
REF
ALT
meta1
sample1
sample2
chr1
1
G
A
BAD
0.1
.
chr1
1
G
A
GOOD
.
0.2
chr1
2
G
T
BAD;GOOD
.
0.1
chr1
2
G
T
GOOD;BAD
0.5
.
Suggest pivoting with only CHROM, POS, REF, ALT. Then add metadata columns back with a left join. Columns from the right dataset in the join should be merged on CHROM, POS, REF, ALT.
When pivoting and including metadata columns, if metadata columns are different for some samples for the same variant, they will be reported separately.
Suggest pivoting with only CHROM, POS, REF, ALT. Then add metadata columns back with a left join. Columns from the right dataset in the join should be merged on CHROM, POS, REF, ALT.