Thank you for your thorough reply. I think you are right about there being a mismatch; Because I also get a number of errors when I try to proceed with annotation on another tool. However, that other tool seems to be more tolerant to the mismatch and proceeds with the job by skipping approximately 700 variations; interestingly, all of which belong to ch1 and ch2.
There are only two error types that get repeated many times. I am pasting them below for you to see:
reference allele not single, possible indel: chr1 978603 . CCT C 276.87 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-0.508;DP=24;FS=0.000;HRun=0;HaplotypeScore=56.8851;MQ=52.36;MQ0=0;MQRankSum=1.397;QD=11.54;ReadPosRankSum=1.397;SB=-89.83;TI=NM_198576;GI=AGRN;FC=Noncoding GT:AD:DP:GQ:PL:VF:GQX 0/1:17,7:24:99:316,0,784:0.292:99
unrecognizable alternative allele(s): chr1 6530965 . C CG 1983.3 PASS AC=2;AF=1.00;AN=2;DP=52;FS=0.000;HRun=5;HaplotypeScore=101.3783;MQ=59.88;MQ0=0;QD=38.14;SB=-731.61;TI=NM_001042665,NM_001042664,NM_020631,NM_001042663,NM_198681;GI=PLEKHG5,PLEKHG5,PLEKHG5,PLEKHG5,PLEKHG5;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding GT:AD:DP:GQ:PL:VF:GQX 1/1:1,50:52:99:2025,156,0:0.980:99
So do you think these errors are caused by mismatch?
And what do you think is the best course of action? Analyzing the FASTQ file again or resequencing the sample?