Converting .sam to .vcf
I have some files in the .sam format which I obtained after I ran Stampy on some Cancer reads. I now have to convert the .sam files to .vcf files to do some analysis and am clueless on how to do the conversion. Any help or hints would be much appreciated.
-
-
Use samtools with mpileup and use bcftools command:
samtools and bcftools are part of the samtools collection.
PLEASE DO examine the options to each command and understand them.
samtools mpileup -R -d 1000 -l rangehg18.chr -uf hg18.fa test.bam | bcftools view -g - > test.vcf
additional note: you will want to convert your sam into a sorted bam ("test.bam" in the example above)Last edited by Richard Finney; 06-19-2012, 07:34 AM.
-
The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.Today, 06:37 PM -
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
| Topics | Statistics | Last Post | ||
|---|---|---|---|---|
|
0 responses
27 views
0 reactions
|
by SEQadmin2
11-12-2026, 07:59 AM
|
|||
|
0 responses
35 views
0 reactions
|
by SEQadmin2
11-05-2026, 09:25 AM
|
|||
|
2 responses
56 views
0 reactions
|
by kinpict.com
Today, 06:49 PM
|
|||
|
0 responses
175 views
0 reactions
|
by SEQadmin2
10-28-2026, 09:57 AM
|
Comment