[Samtools-help] pileup -vcf insertion/deletion columns

[Somya K. <so...@st...>]

 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


-- 
Stanford University Class of 2019
so...@st...
(408)888-1430