Hi,
I am trying to run PEDDY for the first time.
I have gVCF output from GATK exomesinglesample wdl
The format of the vcf is like this:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT F_001 F_002 F_003
chr1 11719 . A <NON_REF> . . END=12377;AN=6;AC=0 GT:DP:GQ 0/0:0:0 0/0:0:0 0/0:0:0
chr1 12445 . G <NON_REF> . . END=12972;AN=6;AC=0 GT:DP:GQ 0/0:3:0 0/0:5:0 0/0:4:0
chr1 13273 . G C,<NON_REF> 4974.06 . AS_QUALapprox=|1522|0;AS_RAW_BaseQRankSum=|1.0,1|NaN;AS_RAW_MQ=112038.00|106888.00|0.00;AS_RAW_MQRankSum=|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-0.7,1|NaN;AS_SB_TABLE=40,44|40,29|0,0;AS_VarDP=84|69|0;BaseQRankSum=1.057;MQRankSum=-0.619;QUALapprox=1522;RAW_GT_COUNT=0,1,0;RAW_MQandDP=226479,157;ReadPosRankSum=-0.627;VarDP=153;DP=531;AN=6;AC=4,0 GT:AD:DP:GQ:PL:SB 0/1:84,69,0:153:99:1522,0,1821,1774,2028,3802:40,44,40,29 0/1:98,87,0:185:99:1853,0,2190,2146,2451,4597:53,45,46,41 1/1:2,184,0:186:99:4988,551,0,4988,551,4988:1,1,100,84
I
When I run PEDDY I get:
2024-04-30 03:58:46 e4549ed3987b peddy.cli[1] INFO Running Peddy version 0.4.8
2024-04-30 03:58:46 e4549ed3987b peddy.cli[1] INFO ped_check
/opt/conda/lib/python3.7/site-packages/peddy/peddy.py:971: UserWarning: peddy: no hets found for sample F_001
min_depth=min_depth, each=each)
/opt/conda/lib/python3.7/site-packages/peddy/peddy.py:971: UserWarning: peddy: no hets found for sample F_002
min_depth=min_depth, each=each)
/opt/conda/lib/python3.7/site-packages/peddy/peddy.py:971: UserWarning: peddy: no hets found for sample F_003
min_depth=min_depth, each=each)
2024-04-30 03:58:50 e4549ed3987b matplotlib.font_manager[1] INFO generated new fontManager
2024-04-30 03:58:51 e4549ed3987b peddy.peddy[1] INFO plotting
2024-04-30 03:58:52 e4549ed3987b peddy.cli[1] INFO ran in 5.7 seconds
2024-04-30 03:58:52 e4549ed3987b peddy.cli[1] INFO het_check
Traceback (most recent call last):
File "/opt/conda/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/opt/conda/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/conda/lib/python3.7/site-packages/peddy/__main__.py", line 14, in <module>
sys.exit(cli())
File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/peddy/cli.py", line 209, in peddy
in ("ped_check", "het_check", "sex_check")]):
File "/opt/conda/lib/python3.7/site-packages/peddy/cli.py", line 43, in run
prefix=prefix, **kwargs)
File "/opt/conda/lib/python3.7/site-packages/peddy/peddy.py", line 867, in het_check
sites, min_depth=min_depth)
File "cyvcf2/cyvcf2.pyx", line 81, in cyvcf2.cyvcf2.par_het
File "cyvcf2/cyvcf2.pyx", line 809, in cyvcf2.cyvcf2.VCF._finish_het
IndexError: index 0 is out of bounds for axis 0 with size 0
Do I need to reformat the gVCF somehow to be able to run PEDDY?
Hi, I am trying to run PEDDY for the first time. I have gVCF output from GATK exomesinglesample wdl The format of the vcf is like this:
I When I run PEDDY I get:
Do I need to reformat the gVCF somehow to be able to run PEDDY?