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Wrong Ref call being reported in CombineGVCFs
I've got an issue when I run CombineGVCFs to merge a bunch of gvcf samples. I'm getting incorrect REF calls at certain point.
The GATK version is 3.5.
ERROR MESSAGE: The provided variant file(s) have inconsistent references for the same position(s) at 1:183085898, C* vs. T*
tabix extra-gvcf.gvcf.gz 1:183085898-183085898
1 183085898 . T . . . GT:DP:GQ:MIN_DP:PL
tabix sorted.vcf.gz 1:183085898-183085898
1 183085898 . C *, . . DP=3072 GT:AD:DP:GQ:MIN_DP:PL:SB
I also ran a test using an interval file (one bed line of 10 basepairs 1:183085890-183085900) and this returned the correct REF (T) at position 183085898 - alt was without a star. This is perplexing!
I've now started running ValidateVariants on the input to see if it's corrupt in some way and it reports the error:
ERROR MESSAGE: File sorted.vcf.gz fails strict validation: one or more of the ALT allele(s) for the record at position 1:2069681 are not observed at all in the sample genotypes
Pulling this position from the merged file, I see lots of samples with no observations (./.) - don't know if this is an issue:
1 2069681 rs3753242 C T, . . BaseQRankSum=1.69;ClippingRankSum=-2.570e-01;DP=962;MQ=60.00;MQ0=0;MQRankSum=-9.900e-02;ReadPosRankSum=0.167 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:16,15,0:31:99:.:399,0,391,447,436,883:7,9,11,4 ./. ./. ./.:.:31:84:30:0,81,861,81,861,861 ./. ./. ./. ./.:.:41:93:41:0,94,1156,94,1156,1156 ./. ./. ./. ./. ./. ./.:0,51,0:51:99:.:1678,153,0,1678,153,1678:0,0,30,21 ./. ./.:0,35,0:35:99:.:1194,105,0,1194,105,1194:0,0,17,18 ./. ./.:.:36:99:36:0,99,1485,99,1485,1485 ./.:18,20,0:38:99:.:474,0,339,526,399,925:9,9,11,9 ./. ./. ./. ./.:.:36:67:36:0,68,870,68,870,870 ./. ./. ./. ./.:16,13,0:29:99:.:357,0,411,405,450,855:9,7,0,13 ./. ./. ./. ./.:0,44,0:44:99:.:1390,131,0,1390,131,1390:0,0,25,19 ./. ./.:19,15,0:34:99:.:363,0,470,421,514,935:10,9,8,7 ./. ./. ./. ./. ./. ./. ./.:20,12,0:32:99:.:305,0,501,365,537,902:8,12,4,8 ./. ./. ./. ./. ./. ./. ./.:.:29:50:29:0,51,743,51,743,743 ./.:23,15,0:38:99:.:386,0,547,454,592,1047:11,12,7,8 ./.:15,16,0:31:99:.:393,0,360,438,407,845:8,7,7,9 ./.:.:33:98:33:0,95,972,95,972,972 ./. ./. ./. ./. ./.:.:33:88:33:0,88,972,88,972,972 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.:24,15,0:39:99:.:368,0,608,440,653,1093:13,11,8,7 ./. ./. ./. ./. ./.:.:31:67:31:0,67,944,67,944,944 ./. ./. ./. ./.:.:35:86:35:0,87,1033,87,1033,1033 ./. ./.:11,23,0:34:99:.:647,0,247,680,316,997:6,5,13,10 ./.:17,15,0:32:99:.:418,0,434,469,479,949:9,8,9,6 ./. ./.:13,13,0:26:99:.:368,0,295,406,334,740:7,6,5,8 ./. ./.:.:35:87:35:0,87,945,87,945,945 ./. ./.:.:24:45:24:0,45,643,45,643,643 ./. ./.:.:38:95:38:0,95,997,95,997,997 ./.:.:34:90:34:0,90,923,90,923,923 ./. ./. ./. ./. ./.:13,17,0:30:99:.:491,0,313,530,364,894:4,9,10,7
Has anyone had this issue before or could maybe tell me if my commands below are wrong.
Thanks in advance for your time,
java -jar /usr/local/bin/GATK.jar -T CombineGVCFs -V HMHMCCCXX_s1_1_GSLv3-7_01_SL146599.realigned.recalibrated.g.vcf.gz -V HMHMCCCXX_s2_1_GSLv3-7_02_SL146600.realigned.recalibrated.g.vcf.gz -V HMHMCCCX
X_s3_1_GSLv3-7_03_SL146601.realigned.recalibrated.g.vcf.gz -V HMHMCCCXX_s4_1_GSLv3-7_04_SL146602.realigned.recalibrated.g.vcf.gz ..... -R hs37d5.fa -o merged.vcf -L intervals.bed