I am trying to use Haploview command line software to compute haplotypes and extract tagSNP for those. When I use the standalone version on my local computer I tick the 'Show tags in blocks' option so that when I export my haplotypes I get the tagSNP to be marked with '!'.

I am trying to do the same thing with the command line version but can't find how to achieve that. My command is as follow (submitted to Linux running server):

java -XX:+UseParallelGC -XX:ParallelGCThreads=1 -jar haploview.jar -nogui \
                    -pedfile $pedfile \
                    -info $info \
                    -out $out  \
                    -maxDistance 100 \
                    -skipcheck \
                    -missingCutoff 0.5 \
                    -blockoutput GAB \
                    -dprime \
                    -log ${out}.log \
                    -memory 124000 \
                    -aggressiveTagging \
                    -aggressiveNumMarkers 3 \
                    -taglodcutoff 3 \
                    -tagrsqcounts \
                    -tagrsqcutoff 0.8 ;

I manually set arguments to the same value when using the standalone version so the only thing differing seems to be the 'Show tags in blocks' option.

Could you explain me how to get the tags to be marked in the *.GABRIELblocks files or how to do it myself using other output files ?

Thanks a bunch !


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