1000 genome SNP call

[heekim1]

mpileup generates only chr1 in a bcf file

I think you're right, the error is in the name of the reference sequence. Check to see the chromosome names in the alignment and reference are _exactly_ the same. We have had this problem frequently.

Hi,
I had a similar situation.
I have a bam file containing read maps across entire chromosomes.
I did mpileup,

samtools mpileup -uf Homo_sapiens_assembly18.fasta s_4.merged.sorted.rmdup.bam | bcftools view -cvbg - > s_4.merged.sorted.rmdup.bam.raw.bcf

by using bcftools view s_4.merged.sorted.rmdup.bam.raw.bcf > s_4.merged.sorted.rmdup.bam.raw.vcf,

I realized that the .vcf file has SNP information on only chr1.
there is no chr2, chr3, ... or chrX

Do you have any idea about this problem?

As you suggested, i checked the chromosome name in both reference sequence and bam file. the name is identical.

Here is a part of my .fai derived from the reference sequence:
chrM 16571 6 50 51
chr1 247249719 16915 50 51
chr2 242951149 252211635 50 51
chr3 199501827 500021813 50 51
chr4 191273063 703513683 50 51
chr5 180857866 898612214 50 51
:
:

Here is a part of my .bam file:
HWI-EAS276_0022_FC70B81AAXX:4:91:4774:3269#0/1 0 chr1 12060 255 34M * 0 0 CTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATG BB=B=DD;DBBBBBDEEDD?ABABEDFEFGGG@G XA:i:0 MD:Z:34 NM:i:0

:
:
HWI-EAS276_0022_FC70B81AAXX:4:29:16345:8488#0/1 16 chr2 34145 255 34M * 0 0 TCATAGTTCTGCTAGACTTCTCTGAGGTGAGCTA @IGDIGIHDIIIIHIIIIGIIIIIIIIHGIIIII XA:i:0 MD:Z:34 NM:i:0
HW
:
:
HWI-EAS276_0022_FC70B81AAXX:4:63:1614:2851#0/1 0 chr3 90279 255 34M * 0 0 TTTTATAAGGGGCTTTTCCCCCTTTGCTCAGCAC IIIIHIDIIIHHIIIIIIIIIIDIIIIHBHHHGH XA:i:0 MD:Z:34 NM:i:0


Thank you

Hee

[colindaven]

I think you're right, the error is in the name of the reference sequence. Check to see the chromosome names in the alignment and reference are _exactly_ the same. We have had this problem frequently.

[zhanglu295]

Thank you very much for your help.

Because I just want to call SNP for each individual separately, so the command used is:

samtools pileup -vcf ref.fa aln.bam > raw.pileup

I think it should be the issue of reference sequence, which I used for snp call is UCSC hg19. Maybe I can test whether this problem still exist after changing the reference sequence.

[ulz_peter]

Just a quick guess:
Samtools homepage recommends snp calling with the following command:

1. samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
2. bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

One possible cause for your problem could lie in the reference sequence. 1000genomes use reference sequences called 1,2,3,4,5,6,etc for the chromosomes
If you use chr1,chr2,chr3 (UCSC-style) reference sequence, that could possibly lead to an empty pileup file.

[ulz_peter]

Could you give the exact command of you SNP calling step?

[zhanglu295]

I want to call SNPs from the 1000 genome project original .bam files

Such as the data we can download from:

ftp://ftp.1000genomes.ebi.ac.uk/vol1...096/alignment/

I used samtools to call SNPs from the bam file named "HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam" in this folder.

but the pileup file is empty, the snp call procedure should be correct, is the bam file incompleted or other potential problems?

Please give me some advise.

Thank you very much

Eric