Hi,
I'm trying to use Tredparse against some samples aligned on hg19_nochr. The calling seems to works fine (ends without errors). However, reports are outputs on hg38 coordinates and samples are always treated as females (the gender can't be inferred).
Here is my code:
tred.py samples.csv --ref hg19_nochr --workdir test
tredreport.py test/*.json --tsv test.tsv --ref hg19
And here are some output.
AX1401.tred.vcf.gz:
X 146993569 FXTAS CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG . . END=146993628;MOTIF=CGG;NS=1;REF=20;CR=55;IH=XLD;RL=60;VT=STR;RPA=30 GT:GB:FR:PR:RR:DP:FDP:PDP:RDP:PEDP:CI:PP:LABEL 1/1:30/30:30|8:4|1;5|2;7|1;8|1;10|2;12|1;13|3;14|2;18|1;20|2;22|1;24|1;25|1;26|1;30|1:50|1:24.8762135922:8:21:1:19:30-30|30-65:0.1425:ok
test.tsv.cases.txt:
[FXTAS] - Fragile X-associated tremor/ataxia syndrome
rep=CGG inherit=XLD cutoff=55 n_risk=8 n_carrier=0 loc=chrX:147912051-147912110
SampleKey inferredGender FXTAS.calls FXTAS.FR FXTAS.PR FXTAS.RR FXTAS.PP
AX1401 Unknown 30|57 30|7 ...|3;26|1;29|1;30|5;32|2;33|1 50|3 0.821746
tred.py --version
tred.pyc 0.7.8
Note: in the VCF file, the coordinates are correctly mapped to FXTAS on hg19, but in the report file corresponds to hg38.
Hi,
I'm trying to use Tredparse against some samples aligned on hg19_nochr. The calling seems to works fine (ends without errors). However, reports are outputs on hg38 coordinates and samples are always treated as females (the gender can't be inferred).
Here is my code:
tred.py samples.csv --ref hg19_nochr --workdir testtredreport.py test/*.json --tsv test.tsv --ref hg19And here are some output.
AX1401.tred.vcf.gz:
test.tsv.cases.txt:
tred.py --versionNote: in the VCF file, the coordinates are correctly mapped to FXTAS on hg19, but in the report file corresponds to hg38.