Alt Contig tutorial question
Answered
Hi!
I am currently looking at the GATK tutorial for "(How to) Map reads to a reference with alternate contigs like GRCH38" (https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38#6.2) and I noticed that in workflow 3, there is an input file called altalt.sam but I do not know where this file came from. There is no prior reference to this file in the tutorial so I am wondering if altalt.sam is the same as 8017bwamem.sam from bwa mem in the tutorial? If so, then the output from this command (k8 bwa-postalt.js) would come directly before steps 4.1-4.7?
Thank you in advance!
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Official comment
Hi Linda Do,
I was looking into this tutorial and I found the summary at the top to have some information about section 6.2:
The third workflow takes the alt-aware alignments from the first workflow and performs a postalt-processing step as well as the same adjustment from the second workflow. Postalt-processing uses the bwa-postalt.js javascript program that Heng Li provides as a companion to BWA. This allows for variant calling on all alternate contigs including HLA alternate contigs.
It looks like the altalt.sam is the alt aware alignment from the first workflow, which would be the output from step 3. It is not before or after steps 4, 5, or 6.1, but it is an alternative method. You can read more at the top of the tutorial for more information about the three different variant calling methods in the tutorial.
Does this help to answer your question?
Best,
Genevieve
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Hi,
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Thank you for your answer. So for clarification, does this mean that the correct workflow 3 would be:
bwa mem chr19chr19KI270866v1alt.fasta 8017read1.fq 8017read2.fq > 8017bwamem.sam
k8 bwa-postalt.js chr19_chr19_KI270866v1_alt.fasta.alt \ 8017bwamem.sam > altalt_postalt.samand since you said it does not come before steps 4,5, and 6.1, this would be it? just 2 commands?
So when the tutorial said:
The resulting postalt-processed SAM,
altalt_postalt.sam, undergoes the same processing as the first workflow (commands 4.1 through 4.7) except that (i) we omit--max_alternate_alleles 3and--read_filter OverclippedReadoptions for the HaplotypeCaller command like we did in section 6.1 and (ii) we perform the 0x1 flag removal step from section 6.1.I should ignore this paragraph?
Thank you in advance
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Hi Linda Do,
Ah, I see! No, I was incorrect before, follow the tutorial and do the processing it recommends to call variants.
Sorry about the confusion.
Best,
Genevieve
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So for clarification, so altalt.sam is indeed the same as 8017bwamem.sam? And these 2 commands should indeed come before steps 4 through 6.1?
Thank you in advance!
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Yes, that looks right! Though I am not the original author of the tutorial, but it looks to be the correct way to interpret it.
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Thank you for your help!
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