0_Unfixed_SNPs_Calling.sh: $markkept file ?

[weiju]

Hi, when running the unfixed SNP calling pipeline, we are running into a problem that the $markkept file is not found. I assumed it is a file .markkept, but that does not seem to be the case. Could you please let me know what the file is supposed to be named and where it is generated ?

#extract unfixed SNPs from forup files, this will create two files: "markdisc" and "markkept"; the suspected false positives(such as mutations with tail region enrichment) will be moved to markdisc file
perl ~/script/mix_extract_0.95.pl $forup > $mix;
perl ~/script/forup_format.pl $mix > $mixfor;
perl ~/script/info_mark.pl $mixfor > $mixmark;
perl ~/script/redepin_filt.pl Excluded_loci_mask.list $dep $mixmark

[weiju]

These are the lines of the script that are troublesome because of the missing $markkept file:

perl ~/script/unfix_scripts/repeatloci_filter.pl 5up_remove_loc.list $markkept > $keptfilt
#annotation of unfixed SNPs
cut -f9-11 $keptfilt > $keptsnp
perl ~/script/1_MTBC_Annotation_mtbc_4411532.pl $keptsnp > $keptanofilt

Thanks !

[MtbEvolution]

"perl ~/script/redepin_filt.pl Excluded_loci_mask.list $dep $mixfor” should create two files including “markkept” and “markdisc”.

On Dec 15, 2023, at 14:22, Wei-ju Wu @.**@.>> wrote:

These are the lines of the script that are troublesome because of the missing $markkept file:

perl ~/script/unfix_scripts/repeatloci_filter.pl 5up_remove_loc.list $markkept > $keptfilt

annotation of unfixed SNPs

cut -f9-11 $keptfilt > $keptsnp perl ~/script/1_MTBC_Annotation_mtbc_4411532.pl $keptsnp > $keptanofilt

Thanks !

— Reply to this email directly, view it on GitHubhttps://github.com/MtbEvolution/resR_Project/issues/4#issuecomment-1858377796, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZVZDOUULG4V6L67ZYOFILTYJSPN7AVCNFSM6AAAAABAW2ZQ2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJYGM3TONZZGY. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[weiju]

Thanks, now it makes sense !