pseq error in DATA.locus_complexity.txt

[fjpt...@outlook.com]

hi:
i follow the xhmm steps,when this command the output file is different with the example file:
pseq . loc-stats --locdb ../EXOME.targets.LOCDB --group targets \
--seqdb plinkseq-0.10/plinkseqdatabase/seqdb.hg19 |awk '{if (NR > 1) print $_}' | sort -k1 -g | awk '{print $10}' | paste XX_Roche.bed - |awk '{print $1"\t"$2}' > ../DATA.locus_complexity.txt
 

example:


my:


so,why this ?

[iastro...@flatironinstitute.org]

Hi,

This is what worked for me at the end:
   change the last part of that line (starting from awk '{print $1"\t"$2}' > ./DATA.locus_complexity.txt) to

    awk '{printf("%s:%d-%s\t%s\n",$1,$2+1,$3,$4);}' > ./DATA.locus_complexity.txt

The first problem is because your targets in BED format(rather than  list), so you need to reformat the line.
The second problem is that xhmm would expect targets with starting coordinate lifted by 1, otherwise, it would not recognize it in the next(filtering) step.
That's why the starting coordinate is upgraded by adding 1 to it.
 
Regards,

    Irina