XPEHH output file blank in SELSCAN · Biostar

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XPEHH output file blank in SELSCAN

I make a SELSCAN input file as .vcf file and a .map file with two population for XPEHH calculation. Reference population files contain the exact same loci as the non-reference file. When I run the XPEHH calculation command, then always make a blank output file only containing file heading. In the output log file, showing two types of warning..........

WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at AX-169366224 WARNING: Reached a gap of 227874bp > 200000bp. Skipping calculation at AX-169366643

Anyone have experience with this type of error?

snp

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updated 7.3 years ago by Biostar

• written 7.5 years ago by azizul •

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