Hi Marc,
thank you for providing an example. This indeed looks like a limitation
of samtools, it does not handle correctly indels like 5D0M6I. I'll
take a look and see if it can be improved.
Cheers,
Petr
On Tue, 2014-10-21 at 14:34 +0200, Marc Sturm wrote:
Hi all,
we use samtools for
i'm struggling to include MQ in my version 1.1 mpileup vcf output.
this used to be easy with the samtools version that i used previously.
maybe i'm missing something simple.
my whole command looks a little like this, and doesn't give MQs:
samtools mpileup -g -I -f b37.fa bam1.bam bam2.bam -l
The new command is `bcftools call`, sorry for the confusion.
petr
On Wed, 2014-10-29 at 13:00 +, the all-new magic tortoise z wrote:
i'm struggling to include MQ in my version 1.1 mpileup vcf output.
this used to be easy with the samtools version that i used previously.
maybe i'm
On Wed, Oct 29, 2014 at 4:01 PM, Daofeng Li lid...@gmail.com wrote:
Hi Alec,
Yes, somehow I also found this right after I sent out the email
So if I want to filter this kind of alignment out, is there a flag could
use?
Yes, use the 0x800 FLAG bit value, e.g. samtools view with the -f or
Hi Peter,
Thanks for the flag value and filed issue.
ha...66% vs 86% mapping rate to me is not slightly different though...might
be I should go with mem
Daofeng
On Wed, Oct 29, 2014 at 11:13 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Wed, Oct 29, 2014 at 4:01 PM, Daofeng Li
Hello,
Could someone comment on the below question. Any suggestions are
valuable.sasaaa
Forwarded Message
Subject:[Samtools-help] N in ALT column
Date: Tue, 28 Oct 2014 15:19:56 +0200
From: mehar meharji.arumi...@helsinki.fi
To:
To loop over FORMAT fields, you need the square brackets, so:
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%DPR\t%DP4]\n' results.vcf
Shane
On 29 Oct 2014, at 19:28, Thomas W. Blackwell wrote:
The manpage for bcftools annotate -c suggests trying something like:
bcftools query
HI Tom,
Good find! Unfortunately, that didn't help, bcftools query doesn't
seem to recognize the suggested syntax of FORMAT/DP4, if I've constructed
the request in the appropriate manner.
$bcftools_htslib_path/bcftools query
-f'%CHROM\t%POS\t%REF\t%ALT\t%DPR\t%FORMAT/DP4\n' results.vcf |
Hi,
I am finding I can't rely on mpileup to report what is happening at each
position (described in a bed file) in a .bam file. Some positions are
omitted and I can't predict the reason this occurs. Example below:
# First, make a small bed file:
cat smallBed.bed
2 186689185 186689205
2
