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== Variant Calling Pipeline FAQs ==
== Variant Calling Pipeline FAQs ==
=== Targetted/Exome ===
; Exiting due to ERROR<nowiki>:</nowiki><br /> INVALID_SORT<nowiki>:</nowiki> ERROR<nowiki>:</nowiki> File is not coordinate sorted at record 1003<br /> PreviousRecord was 1<nowiki>:</nowiki>15347, but this record is 1<nowiki>:</nowiki>15328
: This error occurs if you have <code>SAMTOOLS_VIEW_TARGET_ONLY = TRUE</code> in your configuration file and a read(s) in your BAM file overlaps multiple regions in your BED file.
: To fix this, set<nowiki>:</nowiki>
:: <pre>SAMTOOLS_VIEW_TARGET_ONLY = FALSE</pre>
:Further Explanation of the issue<nowiki>:</nowiki>
::The SAMTOOLS_VIEW_TARGET_ONLY set to TRUE tells our pipeline to pass to SAMTOOLS view all of the regions in the BED file that fall into a single segment of our processing.
::It appears that samtools view will then go through each of those regions independently and one a ta time, selecting just the records that fall within that region.
::A problem occurs if records fall within multiple regions from the BED file. Since samtools view process the regions independently, it will write those records multiple times and they will end up out of order.
::For example<nowiki>:</nowiki>
::: If we have BED with regions chr20 20300049-20300050 and chr20 20300052-20300053
:::The resulting call to samtools view looks like this:
::: <pre>gotcloud/bin/samtools-hybrid view -q 20 -F 0x0704 bamFile.bam 20:20300049-20300050 20:20300052-20300053</pre>
:::Say there are reads at positions 20299969 and 20299994 that are each 76 bases long, they will end up being output twice by the samtools view call and in this order:
::::20299969
::::20299994
::::20299969
::::20299994
== Tutorial FAQs ==
== Tutorial FAQs ==
