problem with reference genome (hg19_nochr)

[erdanieee]

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.