Originally posted by colindaven
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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
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