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Revision as of 10:23, 26 June 2014
, 10:23, 26 June 2014→Examining GotCloud SnpCall Input files
We looked at them yesterday, but you can take another look at the chromosome 22 reference files included for this tutorial:
We looked at them yesterday, but you can take another look at the chromosome 22 reference files included for this tutorial:
ls ${REF}
ls ${SS}/ref22
<ul>
<ul>
The alignment pipeline only processed 4 samples, but for snpcall, we want to run on 62 samples.
The alignment pipeline only processed 4 samples, but for snpcall, we want to run on 62 samples.
* The other 58 samples were already aligned:
* The other 58 samples were already aligned:
ls ${IN}/bams
ls ${SS}/bams
Look at the BAM index for those BAMs:
Look at the BAM index for those BAMs:
less ${IN}/bams/bam.index
less ${SS}/bams/bam.index
Remember, use <code>'q'</code> to exit out of <code>less</code>
Remember, use <code>'q'</code> to exit out of <code>less</code>
We need to add these BAMs to our index
We need to add these BAMs to our index
* Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline
* Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline
cat ${IN}/bams/bam.index >> ${OUT}/bam.index
cat ${SS}/bams/bam.index >> ${OUT}/bam.index
* ">>" will append to the file that follows it
* ">>" will append to the file that follows it
* Be sure to do this command just once
** Check that your BAM index is the correct size
**:<pre>wc -l ${OUT}/bam.index</pre>
*** <code>wc -l</code> counts the number of lines in the file
*** Should be 62
Verify your BAM index contains the additional BAMs
Verify your BAM index contains the additional BAMs
