I am doing research on the BEAN1 repeat. This repeat may have different repeat sequences in the same region, such as "TAGAA, TGGAA, TAAAA". The repeat sequence also affects the pathogenicity of the repeat. When I want to investigate pathogenic repeat, changing the locus structure with pathogenic repeat unit (TGGAA) has almost no effect on the result. Even when I write something of the same length but meaningless, like "HASAN", the result is still the same. What does regex used to find repeats do and how does it work?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002.GRCh38.2x250
chr16 66490398 . A <STR8>,<STR17> . PASS END=66490453;REF=11;RL=55;RU=TGGAA;VARID=BEAN1;REPID=BEAN1 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:19/18:20/24:0/0:61.009132
chr16 66490398 . A <STR8>,<STR17> . PASS END=66490453;REF=11;RL=55;RU=TAAAA;VARID=BEAN1;REPID=BEAN1 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:20/16:19/25:0/0:60.867580
chr16 66490398 . A <STR8>,<STR17> . PASS END=66490453;REF=11;RL=55;RU=TRRRA;VARID=BEAN1;REPID=BEAN1 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:20/16:19/25:0/0:60.867580
chr16 66490398 . A <STR8>,<STR17> . PASS END=66490453;REF=11;RL=55;RU=HASAN,VARID=BEAN1;REPID=BEAN1 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:19/16:19/24:0/0:60.726027
Although the RU field changed, the result remained almost unchanged
I tried;
"LocusStructure": "(TAAAA)"
"LocusStructure": "(TGGAA)"
"LocusStructure": "(TRRRA)"
"LocusStructure": "(HASAN)"
I am doing research on the BEAN1 repeat. This repeat may have different repeat sequences in the same region, such as "TAGAA, TGGAA, TAAAA". The repeat sequence also affects the pathogenicity of the repeat. When I want to investigate pathogenic repeat, changing the locus structure with pathogenic repeat unit (TGGAA) has almost no effect on the result. Even when I write something of the same length but meaningless, like "HASAN", the result is still the same. What does regex used to find repeats do and how does it work?
Repeat's gnomad link = https://gnomad.broadinstitute.org/short-tandem-repeat/BEAN1?dataset=gnomad_r4
Although the RU field changed, the result remained almost unchanged I tried; "LocusStructure": "(TAAAA)" "LocusStructure": "(TGGAA)" "LocusStructure": "(TRRRA)" "LocusStructure": "(HASAN)"