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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Merge adjacent sites into a complex #2229

Open xfk274280 opened 3 months ago

xfk274280 commented 3 months ago

17 37880996 . T TTTA . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2337,1597|178,137;DP=4390;ECNT=2;GERMQ=93;MBQ=35,36;MFRL=184,191;MMQ=60,60;MPOS=26;NALOD=2.09;NLOD=506.28;POPAF=6.00;TLOD=1053.35
17 37880997 . G T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2337,1597|178,137;DP=4408;ECNT=2;GERMQ=93;MBQ=35,34;MFRL=184,191;MMQ=60,60;MPOS=26;NALOD=2.09;NLOD=506.29;POPAF=6.00;TLOD=1053.34

These two sites are close to each other and should be merged into the following format. Can bcftools do it?

17 37880997 . G TTAT . PASS

pd3 commented 3 months ago

Unfortunately not. It is one of the desired features, but it was not implemented yet. See also https://github.com/samtools/bcftools/issues/1843