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MinzhuXie / H-PoPG

H-PoP and H-PoPG: Heuristic Partitioning Algorithms for Single Individual Haplotyping of Polyploids
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lots of repeated variants #6

Closed sinamajidian closed 4 years ago

sinamajidian commented 4 years ago

Dear H-PoPG team I've run the algorithm using following line

java -jar H-PoPG.jar -p 4 -f frag.txt -o phased.txt

One haplotype block contains lots of repeated variant:

27701   4256472 0   1   1   0
27702   4256591 0   1   0   0
27703   4256795 0   1   0   0
27704   4257106 0   1   0   0
..
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0
27769   4261791 0   1   0   0

The number of unique variants is

cat block.txt | cut -f 1 | sort | uniq | wc -l
91

Do have any idea how I can avoid that?

sinamajidian commented 4 years ago

Sorry my bad.