Consensus part from sequence read(fastq) and align(BAM) files

[culmen]

HI,

I am a newbie to NGS data.

Could you guys suggest me the tools to get the part (ex: chr8:125976061-125976501) of consensus and SNP data from the reads and bam files present at 1000genomes ftp site.

Appreciate your suggestion/help,

Thanks,
Culmen

[maubp]

Using 'samtools view' works with a BAM file on FTP, see:
http://samtools.sourceforge.net/samtools.shtml

e.g. To extract that part of chromosome 8 from this BAM file, as SAM format,

$ samtools view ftp://ftp-trace.ncbi.nih.gov/1000gen...d.20100311.bam 8:125976061-125976501

If you had first downloaded the BAM file (and its index), it would just be:

$ samtools view NA20828.chrom8.ILLUMINA.bwa.TSI.exon_targetted.20100311.bam 8:125976061-125976501

The only tricky bit was working out how the reference sequences were named - it turns out chromosome 8 is just "8", rather than "chr8", "chrom8", etc.

[culmen]

I would like to get that in the sequence format.

Thanks a lot for the relpy.

I would like to get that in the sequence format like the consensus sequence shown in the 1000genome browser .
Are there any ways or tools for that.

[maubp]

You can probably compute a consensus from a SAM/BAM file using samtools pileup ... it is late evening here and I don't have samtools installed at home. Perhaps someone else can help?

[culmen]

I was trying to extract consensus from BAM files of 1000genomedata (namely ftp://ftp-trace.ncbi.nih.gov/1000gen...e.20100125.bam 8:125807080-126007080) by samtools pileup consensus calling (ref: hg19 human_g1k_v37.fasta.gz )

I found some bases/positions like bases between position 125906527 and 125906541.

What might be the reason?
Can you guys please help me to obtains those missing bases?

[genesquared]

thanks!

I googled & found this page;
You saved me couple hrs reading the manual page!

Using 'samtools view' works with a BAM file on FTP, see:
http://samtools.sourceforge.net/samtools.shtml

e.g. To extract that part of chromosome 8 from this BAM file, as SAM format,

$ samtools view ftp://ftp-trace.ncbi.nih.gov/1000gen...d.20100311.bam 8:125976061-125976501

If you had first downloaded the BAM file (and its index), it would just be:

$ samtools view NA20828.chrom8.ILLUMINA.bwa.TSI.exon_targetted.20100311.bam 8:125976061-125976501

The only tricky bit was working out how the reference sequences were named - it turns out chromosome 8 is just "8", rather than "chr8", "chrom8", etc.