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andreas-wilm / lofreq3

LoFreq Version 3
MIT License
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deletion bases reported wrongly #2

Closed andreas-wilm closed 4 years ago

andreas-wilm commented 4 years ago

only for len(dels) > 1?

./lofreq pileup -b ../data/spike-in-viterbi.down10p.bam  -f ../data/Ecoli_K12_MG1655_NC_000913.fa -r NC_000913:1685-1685 | ./lofreq call -p -
NC_000913       1685    .       CTGGCG  TGGCG   303     .       AF=0.126984;SB=0;DP=63;DP4=0,0,6,2;TYPE=del

should be


NC_000913       1685    .       CTGGCG  C       100.00  PASS    AC=1;AN=2;SF=0;SOMATIC  GT      0/1     .