I have lots of insertions and deletions that appear in the output files
that I have. From http://samtools.sourceforge.net/cns0.shtml, the sample
they give is in the format
seq2 156 * +AG/+AG 71 252 99 11 +AG * 3 8 0
seq2 157 A A 57 0 99 10 .$.$........ 97<<<<<<<<
seq2 158 A R 18 18 99 8 GG$G..... <;;<<<<<
seq2 159 T T 8 0 99 7 A$A$..... 3:<<<<<
In this example, they say "The line with the 3rd column a star indicates
that the AG insertion is supported by 3 reads; 8 reads agree with the
reference according to the raw alignment; no reads support a third allele.
However, SAMtools infers a AG homozygous insertion with a high score 252
because when we realign the reads with the prior of an insertion, we found
that the 8 reads mapped without gaps are due to a tandam repeat."
In my outputs however, I have more columns following the 3 8 0 that is
printed in their sample. Do you know what the columns after the
tab-delimited * and -G mean? Here is a sample of my output data for
your reference:
seq1 3404636 * */-G 198 198 58 49 *
-G 46 3 0 0 0
seq1 3978142 * */+T 76 76 58 74 *
+T 73 1 0 0 0
seq1 3996202 * */+G 51 51 56 63 *
+G 62 1 0 0 0
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