Curtish@uab.edu at 22:27, 19 December 2011

2011-12-19T22:27:21Z

@@ Line 45: / Line 45: @@
 </pre>
 # For each sample, remove the common SNP rows
-##
+#* I use the workflow [https://galaxy.uabgrid.uab.edu/u/curtish/w/sop-vcffullidx-remove-common-snps SOP: VCF_fullidx remove common SNPs]

Curtish@uab.edu: Created page with "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:..."

2011-12-19T22:04:36Z

Created page with "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:..."

New page

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 =

# For each sample
## Creating the BAM files (usually with BWA + GATK realigner)
## Create VCF of variant SNPs (mpileup or GATK)
## Run snpEffect, compute the "indexAlt" column and extract that index to it's own file
##* I use the workflow a workflow to run [https://galaxy.uabgrid.uab.edu/u/curtish/w/sop-index-snpeffect-with-sample-name SOP: index snpEffect with Sample name], which actually computes several other files and indices need for building an SNP vs Samples grid.
<pre>
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
</pre>
# Concanate idxAlt files from all samples into one file
<pre>
chrLAB:0:chrLAB:JH01_B8M1
chrI:2323:C:T
chrI:2331:A:C
chrI:3981:A:T
...
</pre>
# 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
# Filter to select only records where count()=num_samples
<pre>
2micron:265:G:A 10
chrI:100399:G:C 10
chrI:101282:C:A 10
</pre>
# For each sample, remove the common SNP rows
##

GalaxyFilterCommonSnps - Revision history

Curtish@uab.edu at 22:27, 19 December 2011

Curtish@uab.edu: Created page with "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:..."