Document where the reference sequences came from

[donkirkby]

It's useful to be able to answer questions about the reference sequences, so we should at least have a list of the accession numbers. It might also be helpful to have a script that can fetch them all.

As a start, here's a list of the HCV references from the FDA guidance (PDF):

HCV Genotype	Reference Strain	GenBank Accession ID
Genotype 1a	H77	NC_004102
Genotype 1b	Con1	AJ238799
Genotype 2	JFH-1	AB047639
Genotype 3	S52	GU814263
Genotype 4	ED43	GU814265
Genotype 5	SA13	AF064490
Genotype 6	EUHK2	Y12083

• Compare HIV seeds to HIV compendium.
• Check if we used all references from the HIV compendium.
• Compare HIV coordinate references to HXB2.
• Explain changes from HXB2.
• Compare HCV references.
• Compare HLA references.
• Compare V3LOOP reference used in G2P .
• Remove ERCC references.
• Use HIV Consensus B for resistance wild types.

Configuration changes:

• Upload projects to QAI's pipeline configuration. There are changes in HIV1B-vpr and several HCV seed and coordinate references, plus we removed the ERCC project.

[donkirkby]

I think the HIV references are HXB2 (Accession ID K03455).