Closed ionicbond2005 closed 3 years ago
Hi all,
I try to use SAIGE and I got a problem in step 2.
I have an vcf which was annotated by TabANNO (showing the first variant record)
1 752697 . G A 467.70 PASS AC=1;AF=0.0002341;AN=4272;AS_BaseQRankSum=3.3;AS_FS=0;AS_FilterSt atus=PASS;AS_InbreedingCoeff=-0.0002;AS_MQ=60;AS_MQRankSum=0;AS_QD=11.41;AS_ReadPosRankSum=1.2;AS_SOR=0.818;AS_VQSLOD=19. 1931;AS_culprit=MQRankSum;BaseQRankSum=3.31;DP=82512;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0002;MLEAC=1;MLEAF=0.000234 1;MQ=60;MQRankSum=0;PG=0,33,70;QD=11.41;ReadPosRankSum=1.21;SOR=0.818;ANNO=Intergenic;ANNOFULL=Intergenic GT:AD:DP:GQ: PL:PP 0/0:39,0:39:99:0,105,1575:0,138,1645 0/0:36,0:36:99:0,99,1485:0,132,1555
=========================================================
I also have a group file is shown below (which is made by EPACTS, showing the first two lines):
A1BG 19:58858788_G/C 19:58858800_T/C 19:58858894_CAGCAGCTCGAAG/C 19:58858956_C/A 19:58858964_G/A 19:58858971_T/C 19:58861769_C/T 19:58861938_CT/C 19:58861946_G/A 19:58862024_A/C 19:58862780_G/A 19:58862789_T/G 19:58862822_C/G 19:58862834_G/T 19:58862864_G/A 19:58862915_AG/A 19:58863011_G/C 19:58863649_C/T 19:58863807_C/T 19:58863868_C/G 19:58864329_G/A 19:58864353_C/A,T 19:58864354_G/A 19:58864384_T/C 19:58864391_G/T 19:58864411_G/C 19:58864413_G/A 19:58864425_A/T 19:58864476_A/G 19:58864480_G/A 19:58864560_T/G 19:58864655_C/T 19:58864791_C/T A1BG-AS1 19:58864737_C/T
=======================================================
Then when I run SAIGE, it gives out errors like this
geneID: A1BG Info key not in header: ANNO std::size_t sample_size = marker_file.samples().size();1621 cntMarker: 0 [1] "No markers are left!" .......
caught segfault address (nil), cause 'memory not mapped'
What causing this issue? Any help would be appreciated
Thank you very much Samuel Li
Hi all,
I try to use SAIGE and I got a problem in step 2.
I have an vcf which was annotated by TabANNO (showing the first variant record)
1 752697 . G A 467.70 PASS AC=1;AF=0.0002341;AN=4272;AS_BaseQRankSum=3.3;AS_FS=0;AS_FilterSt atus=PASS;AS_InbreedingCoeff=-0.0002;AS_MQ=60;AS_MQRankSum=0;AS_QD=11.41;AS_ReadPosRankSum=1.2;AS_SOR=0.818;AS_VQSLOD=19. 1931;AS_culprit=MQRankSum;BaseQRankSum=3.31;DP=82512;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0002;MLEAC=1;MLEAF=0.000234 1;MQ=60;MQRankSum=0;PG=0,33,70;QD=11.41;ReadPosRankSum=1.21;SOR=0.818;ANNO=Intergenic;ANNOFULL=Intergenic GT:AD:DP:GQ: PL:PP 0/0:39,0:39:99:0,105,1575:0,138,1645 0/0:36,0:36:99:0,99,1485:0,132,1555
=========================================================
I also have a group file is shown below (which is made by EPACTS, showing the first two lines):
A1BG 19:58858788_G/C 19:58858800_T/C 19:58858894_CAGCAGCTCGAAG/C 19:58858956_C/A 19:58858964_G/A 19:58858971_T/C 19:58861769_C/T 19:58861938_CT/C 19:58861946_G/A 19:58862024_A/C 19:58862780_G/A 19:58862789_T/G 19:58862822_C/G 19:58862834_G/T 19:58862864_G/A 19:58862915_AG/A 19:58863011_G/C 19:58863649_C/T 19:58863807_C/T 19:58863868_C/G 19:58864329_G/A 19:58864353_C/A,T 19:58864354_G/A 19:58864384_T/C 19:58864391_G/T 19:58864411_G/C 19:58864413_G/A 19:58864425_A/T 19:58864476_A/G 19:58864480_G/A 19:58864560_T/G 19:58864655_C/T 19:58864791_C/T A1BG-AS1 19:58864737_C/T
=======================================================
Then when I run SAIGE, it gives out errors like this
geneID: A1BG Info key not in header: ANNO std::size_t sample_size = marker_file.samples().size();1621 cntMarker: 0 [1] "No markers are left!" .......
caught segfault address (nil), cause 'memory not mapped'
What causing this issue? Any help would be appreciated
Thank you very much Samuel Li