GalaxyFilterCommonSnps

From UABgrid Documentation
Revision as of 17:04, 19 December 2011 by Curtish@uab.edu (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Protocol for Filtering common SNPs from a set of alignments

Galaxy supports set operations on single columns. Thus, I build an index column for each sample formated as "chr:pos:ref:alt", which I refer to as the indexAlt.

Tools used

  • Text Manipulation
    • Compute
    • Cut
    • Concatenate Datasets tail-to-head
    • Filter data on any column
  • Join, Subtract and Group
    • Group data by a column
    • Compare two Datasets


Step by Step

  1. For each sample
    1. Creating the BAM files (usually with BWA + GATK realigner)
    2. Create VCF of variant SNPs (mpileup or GATK)
    3. Run snpEffect, compute the "indexAlt" column and extract that index to it's own file
chrLAB	0	.	chrLAB	JH03_B8M2	0	.	JH03_B8M2	JH03_B8M2	JH03_B8M2	JH03_B8M2	JH03_B8M2	chrLAB:0:chrLAB	chrLAB:0:chrLAB:JH03_B8M2
chrI	2323	.	C	T	471.72	.	AC=1;AF=0.50;AN=2;BaseQRankSum=0.330;DP=234;Dels=0.00;FS=21.822;HRun=2;HaplotypeScore=4.4329;MQ=44.55;MQ0=0;MQRankSum=-10.441;QD=2.02;ReadPosRankSum=0.083;EFF=DOWNSTREAM(LOW|||YAL067C|CALC_BIOTYPE||YAL067C|),DOWNSTREAM(LOW|||YAL068
W-A|CALC_BIOTYPE||YAL068W-A|),DOWNSTREAM(LOW|||YAL069W|CALC_BIOTYPE||YAL069W|),UPSTREAM(LOW|||YAL067W-A|CALC_BIOTYPE||YAL067W-A|),UPSTREAM(LOW|||YAL068C|CALC_BIOTYPE||YAL068C|)	GT:AD:DP:GQ:PL	0/1:175,58:234:99:502,0,6142	DOWNSTREAM(LOW|||YAL067C|CALC_BIOTY
PE||YAL067C|),DOWNSTREAM(LOW|||YAL068W-A|CALC_BIOTYPE||YAL068W-A|),DOWNSTREAM(LOW|||YAL069W|CALC_BIOTYPE||YAL069W|),UPSTREAM(LOW|||YAL067W-A|CALC_BIOTYPE||YAL067W-A|),UPSTREAM(LOW|||YAL068C|CALC_BIOTYPE||YAL068C|)	0/1	chrI:2323:C	chrI:2323:C:T
  1. Concanate idxAlt files from all samples into one file
chrLAB:0:chrLAB:JH01_B8M1
chrI:2323:C:T
chrI:2331:A:C
chrI:3981:A:T
...
  1. Group on c1, computing count(c1)
    • this produces one line for every SNP in any sample, with a count of how many samples it appears in
  2. Filter to select only records where count()=num_samples
2micron:265:G:A	10
chrI:100399:G:C	10
chrI:101282:C:A	10
  1. For each sample, remove the common SNP rows
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox