CallSNPs.py - Revision history

Rf at 09:27, 6 October 2017

2017-10-06T09:27:39Z

2017-10-06T09:09:33Z

2017-07-07T12:11:56Z

2017-03-30T15:09:00Z

2017-03-30T14:44:07Z

2017-03-30T14:39:33Z

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@@ Line 147: / Line 147: @@
 ===Filter variants through a maximum read depth ===
   bcftools view ''bcf_file'' | vcfutils.pl varFilter -D''NUM'' > ''outputvcffilename''
-'''bcftools view''' outputs the variants in VCF format and '''vcfutils.pl''' perl script , which is part of samtools platform, filters for variants on their maximum value via the '''-D''' option (the default for this is 10 million, which strikes one as meaning "infinite").
+'''bcftools view''' outputs the variants in VCF format and '''vcfutils.pl''' perl script , which is part of samtools platform, filters for variants on their maximum value via the '''-D''' option (the default for this is 10 million, which strikes one as meaning "infinite"). A more normal value is 1500 (and this is the default value in the original script).
 ===Housekeeping: compress vcf files===

← Older revision		Revision as of 09:09, 6 October 2017
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	The ID lines of the resulting fasta file needs to be cleaned a little to ensure later downstream compatibility.		The ID lines of the resulting fasta file needs to be cleaned a little to ensure later downstream compatibility.
		+
		+	= Links =
		+	* A similar pipeline from [https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf Dan Bolser].

@@ Line 136: / Line 136: @@
 <ins>Comments on original</ins>:
-The original samtools mpileup command had an '''-E''' option at the beginning of the option list. But this is incompatible wi thte '''-B''' which s more important, so it was removed.
+The original samtools mpileup command had an '''-E''' option at the beginning of the option list. But this is incompatible with the '''-B''' which is more important, so it was removed.
 * '''-E''', recalculates BAQ (Base Alignment Quality) as well. The existing BQ tags ae ignored (these are probably previous BAQ values).
 The original bcftools view part included a '''-c''', but:

@@ Line 84: / Line 84: @@
 |Single FASTA file
 |-
-|style="text-align:right;"|'''9.'''
+|style="text-align:right;"|'''10.'''
 |RAxML
 |Gitv4692545

@@ Line 10: / Line 10: @@
   vcf_tab_to_fasta_alignment.pl
 = Pipeline Summary =
@@ Line 59: / Line 58: @@
 |style="text-align:right;"|'''6.'''
 |vcftools
 |Recode VCF files based on intersect regions
 |single intersect BED file
@@ Line 65: / Line 65: @@
 |style="text-align:right;"|'''7.'''
 |bcftools filter
 |Filter out <30 base and <50 mapping quality
 |BCF files
@@ Line 71: / Line 72: @@
 |style="text-align:right;"|'''9.'''
 |vcftools vcf-merge
 |Merge all VCF file into one
 |Multiple recoded VCF files
@@ Line 76: / Line 78: @@
 |-
 |style="text-align:right;"|'''9.'''
 |vcftools
 |Convert merged VCF file to sequences
 |Single VCF files
@@ Line 83: / Line 86: @@
 |style="text-align:right;"|'''9.'''
 |RAxML
 |Calculate tree using Ascertainment Bias
 |Single FASTA file
 |Newick file
 |}
 = How to run =

@@ Line 45: / Line 45: @@
 |style="text-align:right;"|'''4.'''
 |bedtools genomecov
 |Generate high coverage region file
 |BAM files
@@ Line 51: / Line 52: @@
 |style="text-align:right;"|'''5.'''
 |bedtools intersect
 |Find regions common to whole dataset
 |all BED files

@@ Line 14: / Line 14: @@
 = Pipeline Summary =
-{|class="wikitable" style="width:80%"
+{|class="wikitable" style="width:90%"
 |style="width: 3%; text-align:right;"|'''Step'''
 |style="width: 14%"|'''Tool'''
-|style="width: 38%"|'''Operation'''
+|style="width: 4%"|'''Version'''
 |style="width: 25%"|'''Inputs'''
 |style="width: 20%"|'''Outputs'''
 |-
 |style="text-align:right;"|'''1.'''
 |bwa
 |Alignment/Mapping of reads to reference
 |Reference FASTA and FASTQ reads
@@ Line 29: / Line 31: @@
 |style="text-align:right;"|'''2.'''
 |samtools mpileup
 |Calculation of SNP values
 |BAM files
@@ Line 35: / Line 38: @@
 |style="text-align:right;"|'''3.'''
 |bcftools
 |Classification into SNPs
 |BCF files
@@ Line 81: / Line 85: @@
 |Newick file
 |}
 = How to run =

@@ Line 62: / Line 62: @@
 |BCF files
 |VCF files
 |}