3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Sequence Mapping and Assembly Practical, June 2014 (view source)
Revision as of 20:27, 14 June 2014
, 20:27, 14 June 2014→Examining GotCloud Align Output
Let's look at the output directory:
Let's look at the output directory:
ls ${OUTPUT}
ls ${OUT}
[[File:gcalignOutM.png|600px]]
[[File:gcalignOutM.png|600px]]
=== BAM Files ===
Let's look at the BAMs (aligned reads that are ready for variant calling):
Let's look at the BAMs (aligned reads that are ready for variant calling):
ls ${OUTPUT}/bams
ls ${OUT}/bams
[[File:GcalignOutBAMm.png|600px]]
[[File:GcalignOutBAMm.png|600px]]
* Binary Sequence Alignment/Map (SAM) Format
* Binary Sequence Alignment/Map (SAM) Format
* Maps reads to Chromosome/Position
* Maps reads to Chromosome/Position
*** Records - one for each sequence read
*** Records - one for each sequence read
Let's examine a BAM file:
Let's examine a BAM file:
samtools view -h ${OUTPUT}/bams/
samtools view -h ${OUT}/bams/
[[File:BAM.png|750px]]
[[File:BAM.png|750px]]
=== Quality Control Files ===
Let's take a look at our quality control output directory:
Let's take a look at our quality control output directory:
ls ${OUTPUT}/QCFiles
ls ${OUT}/QCFiles
[[File:GcalignOutQCm.png|600px]]
[[File:GcalignOutQCm.png|600px]]
==== Sample Contamination/Swap ====
Check for sample contamination:
Check for sample contamination:
* *.selfSM : Main output file containing the contamination estimate.
* *.selfSM : Main output file containing the contamination estimate.
* *.depthSM : depth distribution of reads covering the marker position of the input VCF, across all readGroups.
* *.depthSM : depth distribution of reads covering the marker position of the input VCF, across all readGroups.
* *.depthRG : depth distribution of reads covering the marker position of the input VCF, per readGroups.
* *.depthRG : depth distribution of reads covering the marker position of the input VCF, per readGroups.
less -S ${OUTPUT}/QCFiles/HG00551.genoCheck.selfSM
less -S ${OUT}/QCFiles/HG00551.genoCheck.selfSM
[[File:Contam1.png|700px]]
[[File:Contam1.png|700px]]
==== QC Metrics ====
Next, let's look at some quality control metrics:
Next, let's look at some quality control metrics:
cat ${OUTPUT}/QCFiles/HG00551.qplot.stats
cat ${OUTPUT}/QCFiles/HG00551.qplot.stats
Generate the pdf's of our quality metrics:
Generate a pdf of quality metrics:
Rscript ${OUTPUT}/QCFiles/HG00551.qplot.R
Rscript ${OUT}/QCFiles/HG00551.qplot.R
Examine the PDF:
Examine the PDF:
evince ${OUTPUT}/QCFiles/HG00551.qplot.pdf&
evince ${OUT}/QCFiles/HG00551.qplot.pdf&
The first plot: Empirical vs reported Phred score does not look as good as we would like.
The first plot: Empirical vs reported Phred score does not look as good as we would like.
* This is due to the small region used for recalibration
* This is due to the small region used for recalibration
Look at the PDF I produced when I ran the whole genome:
Look at the PDF I produced when I ran the whole genome:
evince ${GC}/example/HG00551.wg.qplot.pdf&
evince ${IN}/example/HG00551.wg.qplot.pdf&
See: [[QPLOT#Diagnose_sequencing_quality|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results.
See: [[QPLOT#Diagnose_sequencing_quality|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results.
