view tools/indels/indel_analysis.xml @ 1:cdcb0ce84a1b

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author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
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<tool id="indel_analysis" name="Indel Analysis" version="1.0.0">
  <description></description>
  <command interpreter="python">
    indel_analysis.py
      --input=$input1
      --threshold=$threshold
      --out_ins=$out_ins
      --out_del=$out_del
  </command>
  <inputs>
    <param format="sam" name="input1" type="data" label="Select sam file to analyze" />
    <param name="threshold" type="float" value="0.015" size="5" label="Frequency threshold" help="Cutoff" />
  </inputs>
  <outputs>
    <data format="interval" name="out_del" />
    <data format="interval" name="out_ins" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="indel_analysis_in1.sam" ftype="sam"/>
      <param name="threshold" value="0.017"/>
      <output name="out_del" file="indel_analysis_out1.interval" ftype="interval"/>
      <output name="out_ins" file="indel_analysis_out2.interval" ftype="interval"/>
    </test>
    <test>
      <param name="input1" value="indel_analysis_in2.sam" ftype="sam"/>
      <param name="threshold" value="0.09"/>
      <output name="out_del" file="indel_analysis_out3.interval" ftype="interval"/>
      <output name="out_ins" file="indel_analysis_out4.interval" ftype="interval"/>
    </test>
  </tests>
  <help>

**What it does**

Given an input sam file, this tool provides analysis of the indels. It filters out matches that do not meet the frequency threshold. The way this frequency of occurence is calculated is different for deletions and insertions. The CIGAR string's "M" can indicate an exact match or a mismatch. For SAM containing the following bits of information (assuming the reference "ACTGCTCGAT")::

 CHROM  POS   CIGAR  SEQ
   ref    3  2M1I3M  TACTTC
   ref    1  2M1D3M  ACGCT
   ref    4  4M2I3M  GTTCAAGAT
   ref    2  2M2D3M  CTCCG
   ref    1  3M1D4M  AACCTGG
   ref    6  3M1I2M  TTCAAT
   ref    5  3M1I3M  CTCTGTT
   ref    7      4M  CTAT
   ref    5      5M  CGCTA
   ref    3  2M1D2M  TGCC

The following totals would be calculated (this is an intermediate step and not output)::

 -------------------------------------------------------------------------------------------------------
  POS  BASE  NUMREADS  DELPROPCALC  DELPROP  INSPROPSTARTCALC  INSSTARTPROP  INSPROPENDCALC  INSENDPROP
 -------------------------------------------------------------------------------------------------------
    1     A         2          2/2     1.00               ---           ---             ---         ---
    2     A         1          1/3     0.33               ---           ---             ---         ---
          C         2          2/3     0.67               ---           ---             ---         ---
    3     C         1          1/5     0.20               ---           ---             ---         ---
          T         3          3/5     0.60               ---           ---             ---         ---
          -         1          1/5     0.20               ---           ---             ---         ---
    4     A         1          1/6     0.17               ---           ---             ---         ---
          G         3          3/6     0.50               ---           ---             ---         ---
          -         1          1/6     0.17               ---           ---             ---         ---
         --         1          1/6     0.17               ---           ---             ---         ---
    5     C         4          4/7     0.57               ---           ---             ---         ---
          T         2          2/7     0.29               ---           ---             ---         ---
          -         1          1/7     0.14               ---           ---             ---         ---
         +C         1          ---      ---               1/7          0.14             1/9        0.11
    6     C         2          2/9     0.22               ---           ---             ---         ---
          G         1          1/9     0.11               ---           ---             ---         ---
          T         6          6/9     0.67               ---           ---             ---         ---
    7     C         7          7/9     0.78               ---           ---             ---         ---
          G         1          1/9     0.11               ---           ---             ---         ---
          T         1          1/9     0.11               ---           ---             ---         ---
    8     C         1          1/7     0.14               ---           ---             ---         ---
          G         4          4/7     0.57               ---           ---             ---         ---
          T         2          2/7     0.29               ---           ---             ---         ---
         +T         1          ---      ---               1/8          0.13             1/6        0.17
        +AA         1          ---      ---               1/8          0.13             1/6        0.17
    9     A         4          4/5     0.80               ---           ---             ---         ---
          T         1          1/5     0.20               ---           ---             ---         ---
         +A         1          ---      ---               1/6          0.17             1/5        0.20
   10     T         4          4/4     1.00               ---           ---             ---         ---

The general idea for calculating these is that we want to find out the proportion of times a particular event occurred at a position among all reads that touch that base in some way. First, the basic total number of reads at a given position is the number of reads with each particular base plus the number of reads with that a deletion at that given position (including the bases that are "mismatches"). Note that deletions of two bases and one base would be counted completely separately. Insertions are not counted in this total. For position 4 above, the reference base is G, and there are 3 occurrences of it along with one mismatching base, A. Also, there is a 1-base deletion and another 2-base deletion. So there are a total of 5 matches/mismatches/deletions, and the proportions for each base are 1/6 = 0.17 (A) and 3/6 = 0.50 (G), and for each deletion it is 1/6 = 0.17.

Insertions are slightly more complicated. We actually want to get the frequency of occurrence for both the associated start and end positions, since an insertion appears between those two bases. Each insertion is regarded individually, and the total number of occurrences of that insertion is divided by the sum of the number of its occurrences and the basic total for either the start or end. So for the insertions at position 8, there are a total of 7 matches/mismatches/deletions at position 8, and two insertions that each occur once, so each has an INSSTARTPROP of 1/8 = 0.13. For the end position there are 5 matches/mismatches/deletions, so the INSENDPROP is 1/6 = 0.17 for both insertions (T and AA).

These proportions (DELPROP and either INSSTARTPROP or INSENDPROP) need to be greater than the threshold frequency specified by the user in order for that base, deletion or insertion to be included in the output.


** Output format **

The output varies for deletions and insertions, although for both, the first three columns are chromosome, start position, and end position.

Columns in the deletions file::

                        Column  Description
 -----------------------------  ---------------------------------------------------------------------------------------------------
  1                      Chrom  Chromosome
  2                      Start  Starting position
  3                        End  Ending position
  4                   Coverage  Number of reads containing this exact deletion
  5       Frequency Percentage  Frequency of this exact deletion (2 and 1 are mutually exclusive, for instance), as percentage (%)

Columns in the insertions file::

                   Column  Description
 ------------------------  -----------------------------------------------------------------------------------------------------------------
  1                 Chrom  Chromosome
  2                 Start  Starting position
  3                   End  Ending position (always Start + 1 for insertions)
  4      Inserted Base(s)  The exact base(s) inserted at Start position
  5              Coverage  Number of reads containing this exact insertion
  6  Freq. Perc. at Start  Frequency of this exact insertion given Start position ("GG" and "G" are considered distinct), as percentage (%)
  7    Freq. Perc. at End  Frequency of this exact insertion given End position ("GG" and "G" are considered distinct), as percentage (%)

Before using this tool, you may will want to use the Filter SAM for indels tool to filter out indels on bases with insufficient quality scores, but this is not required.


-----

**Example**

If you set the threshold to 0.0 and have the following SAM file::

 r327     16   chrM   11   37      8M1D10M   *   0   0             CTTACCAGATAGTCATCA   -+&lt;2;?@BA@?-,.+4=4             XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:0  XO:i:1  XG:i:1  MD:Z:41^C35
 r457      0   chr1   14   37          14M   *   0   0                 ACCTGACAGATATC   =/DF;?@1A@?-,.                 XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:76
 r501     16   chrM    6   23      7M1I13M   *   0   0          TCTGTGCCTACCAGACATTCA   +=$2;?@BA@?-,.+4=4=4A          XT:A:U  NM:i:3  X0:i:1  X1:i:1  XM:i:2  XO:i:1  XG:i:1  MD:Z:28C36G9        XA:Z:chrM,+134263658,14M1I61M,4;
 r1288    16   chrM    8   37      11M1I7M   *   0   0            TCACTTACCTGTACACACA   /*F2;?@%A@?-,.+4=4=            XT:A:U  NM:i:4  X0:i:1  X1:i:0  XM:i:3  XO:i:1  XG:i:1  MD:Z:2T0T1A69
 r1902     0   chr1    4   37      7M2D18M   *   0   0        AGTCTCTTACCTGACGGTTATGA   &lt;2;?@BA@?-,.+4=4=4AA663        XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:1  XO:i:1  XG:i:2  MD:Z:17^CA58A0
 r2204    16   chrM    9    0          19M   *   0   0            CTGGTACCTGACAGGTATC   2;?@BA@?-,.+4=4=4AA            XT:A:R  NM:i:1  X0:i:2  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:0T75           XA:Z:chrM,-564927,76M,1;
 r2314    16   chrM    6   37      10M2D8M   *   0   0               TCACTCTTACGTCTGA   &lt;2;?@BA@?-,.+4=4               XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:1  XO:i:1  XG:i:2  MD:Z:25A5^CA45
 r3001     0   chrM   13   37   3M1D5M2I7M   *   0   0              TACAGTCACCCTCATCA   &lt;2;?@BA/(@?-,$&amp;                XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:1  XO:i:1  XG:i:2  MD:Z:17^CA58A0
 r3218     0   chr1   13   37       8M1D7M   *   0   0                TACAGTCACTCATCA   &lt;2;?@BA/(@?-,$&amp;                XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:1  XO:i:1  XG:i:2  MD:Z:17^CA58A0
 r4767    16   chr2    3   37      15M2I7M   *   0   0       CAGACTCTCTTACCAAAGACAGAC   &lt;2;?@BA/(@?-,.+4=4=4AA66       XT:A:U  NM:i:4  X0:i:1  X1:i:0  XM:i:3  XO:i:1  XG:i:1  MD:Z:2T1A4T65
 r5333     0   chrM    5   37      17M1D8M   *   0   0       GTCTCTCATACCAGACAACGGCAT   FB3$@BA/(@?-,.+4=4=4AA66       XT:A:U  NM:i:4  X0:i:1  X1:i:0  XM:i:3  XO:i:1  XG:i:1  MD:Z:45C10^C0C5C13
 r6690    16   chrM    7   23          20M   *   0   0           CTCTCTTACCAGACAGACAT   2;?@BA/(@?-,.+4=4=4A           XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76             XA:Z:chrM,-568532,76M,1;
 r7211     0   chrM    7   37          24M   *   0   0       CGACAGAGACAAAATAACATTTAA   //&lt;2;?@BA@?-,.+4=442;;6:       XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:2  XO:i:1  XG:i:1  MD:Z:73G0G0
 r9922    16   chrM    4    0       7M3I9M   *   0   0            CCAGACATTTGAAATCAGG   F/D4=44^D++26632;;6            XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76
 r9987    16   chrM    4    0      9M1I18M   *   0   0   AGGTTCTCATTACCTGACACTCATCTTG   G/AD6"/+4=4426632;;6:&lt;2;?@BA   XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76
 r10145   16   chr1   16    0       5M2D7M   *   0   0                   CACATTGTTGTA   G//+4=44=4AA                   XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76
 r10324   16   chrM   15    0       6M1D5M   *   0   0                   CCGTTCTACTTG   A@??8.G//+4=                   XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76
 r12331   16   chrM   17    0       4M2I6M   *   0   0                  AGTCGAATACGTG   632;;6:&lt;2;?@B                  XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76
 r12914   16   chr2   24    0       4M3I3M   *   0   0                     ACTACCCCAA   G//+4=42,.                     XT:A:U  NM:i:0  X0:i:1  X1:i:1  XM:i:0  XO:i:0  XG:i:0  MD:Z:76

The following will be produced (deletions file followed by insertions file)::

 chr1   11   13   1   100.00
 chr1   21   22   1    25.00
 chr1   21   23   1    25.00
 chrM   16   18   1     9.09
 chrM   19   20   1     8.33
 chrM   21   22   1     9.09
 chrM   22   23   1     9.09

 chr2   18   19    AA   1   50.00   50.00
 chr2   28   29   CCC   1   50.00   50.00
 chrM   11   12   TTT   1    9.09    9.09
 chrM   13   14     C   1    9.09    9.09
 chrM   13   14     T   1    9.09    9.09
 chrM   19   20     T   1    7.69    8.33
 chrM   21   22    GA   1    8.33    8.33


  </help>
</tool>