In the Heteroplasmy vcf files reporting the heteroplasmic positions, the DP is reporting the "raw depth": does it mean the number of reads supporting that variant, or the number of reads covering that position in general? Usually for the vcf files the correct answer is the second, but in this case I do not understand, because I also assembled my mitogenomes by mapping and I know that the coverage I have on those positions is much higher than the values I get in the attached files. Also, I made two trials: once I used heteroplasmy function after filtering the reads with the filtering script you provide; another time I used heteroplasmy function without filtering the reads, and in both cases I obtained almost the same coverage on the variants (which is unexpected, since in the non-filtered trial I would expect to have much more reads on the variant position...).
In the Heteroplasmy vcf files reporting the heteroplasmic positions, the DP is reporting the "raw depth": does it mean the number of reads supporting that variant, or the number of reads covering that position in general? Usually for the vcf files the correct answer is the second, but in this case I do not understand, because I also assembled my mitogenomes by mapping and I know that the coverage I have on those positions is much higher than the values I get in the attached files. Also, I made two trials: once I used heteroplasmy function after filtering the reads with the filtering script you provide; another time I used heteroplasmy function without filtering the reads, and in both cases I obtained almost the same coverage on the variants (which is unexpected, since in the non-filtered trial I would expect to have much more reads on the variant position...).
log_1616_het_nofilter.txt Heteroplasmy_1616_het.txt Heteroplasmy_1616_het_nofilter.txt Homoplasmy_1616_het.txt Homoplasmy_1616_het_nofilter.txt log_1616_het.txt