search

twolinin / longphase

GNU General Public License v3.0
99 stars 9 forks source link

Modcall output all modification #41

Closed twolinin closed 9 months ago

twolinin commented 9 months ago

Summary

Modcall can output all detected modification positions by using the --all parameter.

Changes

  1. Add code comments

    • ModCallParsingBam.cpp

  2. Adjustments to Modcall Output

    • Added the '--all' parameter to output all detected modifications in reads. default false.
    • Homozygous variants only recorded MD, UD, and DP counts. The read names covering the variant will not be recorded.
    • High-confidence heterozygous modifications will be recorded as PASS in the FILTER field.
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE
chr1    11027   .       C       N       .       .       RS=P;   GT:MD:UD:DP     1/1:5:5:16
chr1    11028   .       G       N       .       .       RS=N;   GT:MD:UD:DP     0/0:4:8:12
chr1    11083   .       G       N       .       .       RS=N;   GT:MD:UD:DP     0/1:4:6:12
chr1    11434   .       C       N       .       PASS    RS=P;MR=eb459876-8c81-4714-a496-a90ea8be94d2,6ca3a71f-62fd-416e-8c6e-8c4a9c054e1a,0d8b7c68-d98d-4045-a572-82fedac62da5,71b5dfe9-7cd1-4959-b634-b9d162468edb,5db6fcd3-5780-494b-bfdd-4d9d7282d012,6e205f04-560a-4975-932d-dbd60ead695d,ae2238f8-b622-4cb5-8f02-4c3f54ab8ca3,d7ef87d0-bffe-404d-9f10-62eceb0c5121;NR=8249c7c7-fd04-4a4c-985d-2bbcb2030bc4,e3b03dc0-8399-4e1e-bd0d-e5e4e3e2911a,b8dc7af8-9f78-4dac-b8cc-35e157c51621,0b2638c1-8380-48b4-b08c-a6161495ad9d,7b1e5c16-f0a6-47f6-9726-247c762a10ca,ac7ae685-082e-413e-b5a6-b4c12d49a1c2,c0e0c526-e193-4ee2-81d6-1fbe0c970dc1;  GT:MD:UD:DP     0/1:8:7:16