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Old 07-20-2010, 09:18 AM   #1
culmen
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Question Consensus part from sequence read(fastq) and align(BAM) files

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
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Old 07-20-2010, 09:34 AM   #2
maubp
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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.

Last edited by maubp; 07-20-2010 at 09:43 AM. Reason: adding example
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Old 07-20-2010, 10:28 AM   #3
culmen
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Post 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.
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Old 07-20-2010, 01:46 PM   #4
maubp
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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?
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Old 07-21-2010, 10:16 AM   #5
culmen
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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?
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Old 12-21-2010, 04:57 AM   #6
genesquared
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Default thanks!

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




Quote:
Originally Posted by maubp View Post
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.
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