Hello,
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.
Thanks,
Mark Wadsworth
