Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I must admit I just gave up on Casava alignments, just use BWA and I am exploring other aligners.
Leave a comment:
-
I am currently trying to deal with exactly this problem: CASAVA alignments that choke mpileup. We use mpileup output directly for analysis with our own SNP finders, and it works very well with output from a BWA-based aligner (stampy). But with CASAVA output, as stated in another response, mpileup thinks everything is a SNP, all reads with phred scores of 0. This is not the case, fortunately, as the same read data run through stampy produces an alignment file that behaves well with mpileup.
Leave a comment:
-
Double check that the chromosome names in your .bam file match the chromosome names in your fasta. And I'd remake the fa.fai with samtools faidx, see if that completes without an error.
Leave a comment:
-
sdriscoll,
It seems that mpileup looking like:
chr1.fa 3309 N 1 ^NT C
chr1.fa 3310 N 1 G C
chr1.fa 3311 N 1 C F
chr1.fa 3312 N 1 C F
is a bad sign, it looks to me that it is not mapping to the ref. genome properly. I did as you suggested and everything was a SNP.
Leave a comment:
-
How to combine .vcf files into whole genome
This discussion is very useful, but when I run mpileup plus bcftools to produce .vcf files for individual Chrm, I have found no way to combine them into whole genome .vcf file for further processing. vcf-concat seems like it might do it, but it never runs due to diverse errors. Most recent is:
****************************
The use of -1 for unknown number of values is deprecated, please use '.' instead.
FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
****************************
I am running most recent version of samtools (0.1.18) -- has anyone else noticed a mismatch in the FORMAT specs between samtools and vcftools??
Any suggestions at all would be very welcom, this is driving me nuts.
Thanks
Allan Lindh
Leave a comment:
-
or you can try splitting the bam file by chromosome and then calling SNP on them separately.. you could also try starting from the fastq or qseq files, run alignment using something like bwa and then call variants
Leave a comment:
-
try this. mpileup doesn't do too much. bcftools is the program that actually does the SNP calling.
Code:samtools mpileup -uf ../genomes/Homo_sapiens/UCSC/hg18/Sequence/WholeGenomeFasta/genome.fa sorted.bam | bcftools view -bvcg - > sorted.bcf bcftools view sorted.bcf > sorted.vcf head sorted.vcf
Leave a comment:
-
Samtools on Chromosomes Versus Genome
Hi everyone,
Does anybody have experience running samtools on CASAVA alignments?
I am trying to call SNPs using samtools on a CASAVA/illumina alignment.
CASAVA outputs an alignment of the type name_export.txt.gz
and it automatically converts to BAM format when using their SNP caller.
Now I want to call SNPs using Samtools.
The alignment was done using each chromosome individually:
genomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/Chr...
However, the BAM alignment provided by CASAVA is for the whole genome, so then should I use the whole reference genome?:
samtools mpileup -f ../genomes/Homo_sapiens/UCSC/hg18/Sequence/WholeGenomeFasta/genome.fa sorted.bam > sorted.mpileupOutput
the problem is that, in that case the mpileup output doesn't seem to recognize it as I get:
bash-3.2$ head -n 100 sorted.mpileupOutput
chr1.fa 3309 N 1 ^NT C
chr1.fa 3310 N 1 G C
chr1.fa 3311 N 1 C F
chr1.fa 3312 N 1 C F
chr1.fa 3313 N 1 C F
Any ideas??
Thanks in advance,
Ramiro
Latest Articles
Collapse
-
by seqadmin
The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...-
Channel: Articles
08-27-2024, 04:44 AM -
-
by seqadmin
Sequencing mRNA provides a snapshot of cellular activity, allowing researchers to study the dynamics of cellular processes, compare gene expression across different tissue types, and gain insights into the mechanisms of complex diseases. “mRNA’s central role in the dogma of molecular biology makes it a logical and relevant focus for transcriptomic studies,” stated Sebastian Aguilar Pierlé, Ph.D., Application Development Lead at Inorevia. “One of the major hurdles for...-
Channel: Articles
08-07-2024, 12:11 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 08-27-2024, 04:40 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
08-27-2024, 04:40 AM
|
||
New Single-Molecule Sequencing Platform Introduces Advanced Features for High-Throughput Genomics
by seqadmin
Started by seqadmin, 08-22-2024, 05:00 AM
|
0 responses
293 views
0 likes
|
Last Post
by seqadmin
08-22-2024, 05:00 AM
|
||
Started by seqadmin, 08-21-2024, 10:49 AM
|
0 responses
135 views
0 likes
|
Last Post
by seqadmin
08-21-2024, 10:49 AM
|
||
Started by seqadmin, 08-19-2024, 05:12 AM
|
0 responses
124 views
0 likes
|
Last Post
by seqadmin
08-19-2024, 05:12 AM
|
Leave a comment: