Small InDels on NA19240 with SOLiD

OVERVIEW:
The SOLiD System was used to sequence NA19240, and small indels were called for this sample using Corona v2 software. Deletions to size 11 and insertions to size 3 were called.

DETECTION METHOD:
* The SOLiD System was used to sequence NA19240 to about 30x coverage, including a mixture of mate pair reads and fragment reads.
* Paired-end reads for which one read map up to z times to the genome and the second read does not map in the correct position(s) are identified. 
* The second read is remapped to a constrained region of the genome, determined by the expected location given library and pairing parameters, and of the predicted map location of the first read
* Only unique pairs where the 2nd read has an indel (up to size 3 insertion and size 11 deletion) are extracted.
* InDels are called if at least 3 reads independently confirm evidence of an InDel at the same position; if these reads have different start positions; and if these reads contain the InDel at positions not at the extreme end of the read.  

SOFTWARE:
Source code for the mapping and pairing tools (including mapping with InDels) and the InDel detection tool can be downloaded at www.solidsoftwarretools.com in early December 2008.

ORIGINAL DATA:
Data used to call the small InDels is available for download at:
ftp1.solidsoftwaretools.com/disk-b/NA19240/
Login: ftpdl1
Password: ftpdl1

FORMAT:
The small Indel file is in standard GFF v3 file format with optional fields in the final column. Specifically, the format is as follows:

Column 1: “seqid”
The ID of the sequence to which the start and end coordinates refer; in this case, it is the human chromosome number.

Column 2: “source”
Free text qualifier indicating the algorithm or method that generated the feature.  This should be the name of the software that generates the output file.  (Prefix with “AB_”?)

Column 3: “type”
Specifies what kind of SOFA feature it is. This file contains the features insertion_site and deletion.

Columns 4 and 5: “start” and “end”
1-based integer coordinates of the feature (relative to the sequence in column 1. For zero-length features, such as insertion sites, start equals end and the implied site is to the right of the indicated base in the direction of the landmark.

Column 6: “score”
Floating point value representing the quality of the evidence for the feature.

Column 7: “strand”
 “.” meaning strand is not relevant for this feature.

Column 8: “phase”
Translation frame;  “.” since phase is relevant only for CDS features.

Column 9: “attributes”
ins_len	Insertion length
del_len	Deletion length
tight_chrom_pos	Conservative estimate of chromosome position range of the feature.
loose_chrom_pos	Maximum estimate of chromosome position range of the feature.
no_nonred_reads	Number of reads with unique start positions (non-redundant reads) 
no_mismatches	Number of mismatches for each read 
read_pos	Position in each non-redundant read at which the In/Del occurs
strands	Strand for each read
dbSNP	Annotation of any dbSNP InDel entry within 10bp of the InDel
uw_hgsv	Annotation of any U. Washington HGSV InDel entry within 10bp of the InDel

AUTHORS:
Eric Tsung, Zheng Zhang, Heather Peckham, Fiona Hyland, Stephen McLaughlin, Jingwei Ni, Yutao Fu, Francisco De La Vega, Kevin McKernan.

CONTACT:
fiona.hyland@appliedbiosystems.com