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Old 12-14-2010, 02:16 AM   #1
nkwuji
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Default Question on calling SNPs using samtools/bcftools

Hi,

I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is created by:

Code:
samtools mpileup -ugf ref.fa seq.bam >test.bcf
Quote:
chr21 8588396 . T A,X 0 . DP=13;I16=1,9,0,3,378,14392,73,1809,600,36000,180,10800,93,1075,42,642 PL 27,0,57,190,199,232
From PL value, P(D|TT)=10^(-2.7), P(D|TA)=0. So TA allele should be the most possible allele.

But in the processed vcf using this command:

Code:
bcftools view -c test.bcf > test_count.vcf
This SNP is:
Quote:
chr21 8588396 . T . 4.76 . DP=13;AF1=0.4995;CI95=0.5,0.5;DP4=1,9,0,3;MQ=60;PV4=1,5.9e-05,1,1 PL 27
There is no alternative base information, but the AF1 is about 0.5, which means this is an heterozygous allele. And, if I use the following command, there is no SNP called at all.

Code:
bcftools view -vcg test.bcf > test_count.vcf
Why the alternative base is not A??? Is there any option I can choose to call this SNP?

BTW, I am using samtools version 0.1.10-6.

Cheers,

Jun
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Old 12-21-2010, 06:35 AM   #2
nkwuji
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Location: Dublin

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Posts: 19
Default

Quote:
Originally Posted by nkwuji View Post
Hi,

I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is created by:

Code:
samtools mpileup -ugf ref.fa seq.bam >test.bcf


From PL value, P(D|TT)=10^(-2.7), P(D|TA)=0. So TA allele should be the most possible allele.

But in the processed vcf using this command:

Code:
bcftools view -c test.bcf > test_count.vcf
This SNP is:


There is no alternative base information, but the AF1 is about 0.5, which means this is an heterozygous allele. And, if I use the following command, there is no SNP called at all.

Code:
bcftools view -vcg test.bcf > test_count.vcf
Why the alternative base is not A??? Is there any option I can choose to call this SNP?

BTW, I am using samtools version 0.1.10-6.

Cheers,

Jun
Still unsolved... waiting for an answer...
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Old 12-21-2010, 07:40 AM   #3
lh3
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you need to apply the prior
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Old 12-21-2010, 07:47 AM   #4
nkwuji
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Quote:
Originally Posted by lh3 View Post
you need to apply the prior
Hi, Lh3,

Thx for your reply. Could you elaborate it? I find an option in bcttools view

-P STR, type of prior: full, cond2, flat

Do you mean this option? What are the differences between them?

Cheers,
Jun
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Old 01-21-2011, 09:38 AM   #5
LisaM
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Quote:
Originally Posted by nkwuji View Post
Hi, Lh3,

Thx for your reply. Could you elaborate it? I find an option in bcttools view

-P STR, type of prior: full, cond2, flat

Do you mean this option? What are the differences between them?

Cheers,
Jun
Hi, could someone please comment on this please? I'm also looking into the differences between the "prior" commands, and I haven't been able to find anything on the internet. Any information would be helpful.

Thanks!
Lisa
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Old 02-24-2011, 03:58 AM   #6
whodo_voodoo
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Location: Glasgow, UK

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Default

Hi,

Another request here for some more information with regards the 'prior' and snp calling options of bcftools. I've been trying to learn how to change the parameters of the snp calling but can't find much information on how to change the parameters in bcftools.

I've also got a second related question about bcftools, the mpileup page says
Quote:
BCFtools does not properly handle multi-allelic variants. It only takes the strongest non-reference allele.
Does anybody know how much of an issue this is? I'm expecting a number of my SNPs to be heterozygous with no allele match to the reference, will this issue prevent me seeing them?

Thanks in advance for any answers,

Craig
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Old 02-19-2013, 08:52 AM   #7
dan
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Quote:
Originally Posted by lh3 View Post
you need to apply the prior
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