1000 genome data download

[zhanglu295]

I have downloaded the three bam files from

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/

for each individual such as

HG00119.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
HG00119.unmapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam

Then I combined them together to use samtools calling SNP.

But the result (pileup file) did not contain all the chromosomes.

Is it only a truncated file now?

[ulz_peter]

I assume you already changed the reference sequence file names, did you?

[zhanglu295]

Yes, I have used the reference sequence from 1000 genome project form the website:

ftp://ftp.sanger.ac.uk/pub/1000genom...k_v37.fasta.gz

This time I can successfully call SNPs from some chromosomes but not all the chromosomes.

And when I used the samtool index function

such messeage appeared:

[bam_header_read] EOF marker is absent.
[bam_index_core] truncated file? Continue anyway. (-2)

[ulz_peter]

Did you check the MD5 checksum of your downloaded files. Maybe there was something wrong with the download?

How did you combine the three files (just using cat or similar tools wouldn't work as all of them contain headers)?

Did you check the headers of the file. Is every reference sequence in the header section (./samtools view -H)?

[zhanglu295]

Thank you very much for your help.

1. Can you tell me where I can find the MD5 code for bam files from 1000 genome website? I can only find the fastq MD5.

2. I used the samtools merge function to combine this three files(./samtools merge out.bam in1.bam in2.bam in3.bam), is it appropriate here?

3.The head appeared as
"@SQ SN:GL000192.1 LN:547496 AS:NCBI37 UR:ftp://ftp.1000genomes.ebi.ac.uk/vol1...k_v37.fasta.gz M5:325ba9e808f669dfeee210fdd7b470ac SP:Human"
Is it correct?

Sorry for trouble you so much.
I do not have much experience in this field.

Thank you.

[ulz_peter]

1) In the directory of the bam files you'll find a .bas file including a MD5 field

2) that should actually work, providing the header of the first bam file is correct: to be sure try:

samtools view -H in.bam > header.sam
samtools merge -h header.sam out.bam in1.bam in2.bam ....

But be sure that the first in.bam is the mapped bam file

3) Your header does NOT look ok. It should mention every reference sequence so at least 24 entries (including X, Y and MT)...