I am calling variants on mitochondrial genomes using freebayes. I am using the following command:
freebayes -f $REF -p 1 -F 0.6 $BAM | $VCFFILTER -f "QUAL > 20" > $F_6_OUT
I have been playing with the -F thresholds to see which give me the best information. I have found something that I don't understand about how you are calling indels. The following are two lines of the file that I get when I run it with a -F of 0.2:
gi|251831106|ref|NC_012920.1| 302 . ACCCCCCCT ACCCCCCCC 1516.89 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=103;CIGAR=8M1X;DP=242;DPB=444.667;DPRA=0;EPP=6.5732;EPPR
gi|251831106|ref|NC_012920.1| 566 . CA CC 802.756 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=152;CIGAR=1M1X;DP=174;DPB=183;DPRA=0;EPP=123.927;EPPR=30.8051;GTI=0;LEN=
It looks like there is a snp at position 310 from a T to a C and at position 567 A to C. I'm not sure why it is calling these indels.
I get a different call at these positions with a -F of 0.6:
gi|251831106|ref|NC_012920.1| 310 . TCC TCCC 8915.44 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=642;CIGAR=1M1I2M;DP=1024;DPB=1260.67;DPRA=0;EPP=197.834;EPPR=16.2968;GTI
gi|251831106|ref|NC_012920.1| 567 . A C 1238.76 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=170;CIGAR=1X;DP=191;DPB=191;DPRA=0;EPP=88.8984;EPPR=30.8051;GTI=0;LEN=1;
Here it shows the snp at position 567 from A to C but at position 310 it is showing a different insertion. Where 310 stays a T but after there is an extra C.
My question consists of how should I read the information that is given by the indel calls. I have looked for an answer for this and have not had success in finding it. Thanks so much! Let me know if you need any more information from me.