Florian Pauler

createSNPbedfile.sh

createSNPbedfile.sh

2 problems were solved in this ticket: 1) SNPs from C57Bl/6JN can be safely used for any C57Bl/6 strain 2) using bedtools 2.27 solved the problem of empty output files

Hi Carol, Sorry for my sloppy typing - of course it is "intersectBed". Could you provide me the compressed output folder via dropbox or similar ? - in this way I can perhaps trace back the error. best, Florian

Hi Carol, Just to make sure that your environment is correctly configured: Have you installed samtools, bedtools and perl on your system? Can you run intersectbed (from the bedtools suite) from the command line? best, Florian

new version that works with samtools1.x

fix to work with latest samtools version

Hi, Just to clarify: C57Bl/6J and C57Bl/6NJ are not genetically identical - for known differences see https://www.jax.org/strain/005304. However most of the SNPs mapped using C57Bl/6NJ will be identical in C57Bl/6J. Importantly the Allelome.PRO pipeline does identify correctly annotated SNPs by using reciprocal crosses and therefore it is safe to use C57Bl/6NJ for any C57Bl/6 strain. best, Florian