[Useq-users] Header for hg19EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr not matching hg19 used in GATK?

[David N. <Dav...@hc...>]

Hello Jesse,

Yes I've seen this error before.  You'll need to replace the header with
one consistent across all bam files.  There's a picard app that does this
I believe.

The issue is STP generates a custom header on the fly based on the end of
the last alignment in each chromosome.  So the chromosome length differs
for each file.

You can have STP use a particular header with the -r argument for future
parsings.

-cheers, D

On 12/11/12 11:35 AM, "Jesse Rowley" <jes...@u2...> wrote:

>Hi David, 
>I aligned my RNA-seq reads with
>@align -novoalign [-o SAM -r All 50 -a
>AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC] -g
>hg19EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr -i *.txt.gz" > cmd.txt
>this was followed by samtranscriptome parser. Now I ma running GATK.
>
>I get the following error with GATK:
>##### ERROR MESSAGE: Input files reads and reference have incompatible
>contigs: Found contigs with the same name but different lengths:
>##### ERROR   contig reads = chr20 / 62940766
>##### ERROR   contig reference = chr20 / 63025520.
>##### ERROR   reads contigs = [chr20, chr21, chr22, chr5, chr6, chr7,
>chr8, chr9, chr1, chr2, chr3, chr4, chr10, chr11, chr12, chr13, chrY,
>chrX, chr15, chr14, chr17, chr16, chr19, chr18, chrM]
>##### ERROR   reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6,
>chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17,
>chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
>
>These are different as shown below - is it because these are changed by
>maketranscriptome or was this transcriptome made with a different
>reference? should I just revise my Bam header to match or would that be
>problematic? My strategy is to use GATK in the @annot pipeline to
>annotate variants (first splitting out splice junction reads prior to
>indel realignment since GATK doesn't like those, and then remerging them
>before annotation)
>Fasta.fai:
>chr1	249250621	6	50	51
>chr2	243199373	254235646	50	51
>chr3	198022430	502299013	50	51
>chr4	191154276	704281898	50	51
>chr5	180915260	899259266	50	51
>chr6	171115067	1083792838	50	51
>chr7	159138663	1258330213	50	51
>chr8	146364022	1420651656	50	51
>chr9	141213431	1569942965	50	51
>chr10	135534747	1713980672	50	51
>chr11	135006516	1852226121	50	51
>chr12	133851895	1989932775	50	51
>chr13	115169878	2126461715	50	51
>chr14	107349540	2243934998	50	51
>chr15	102531392	2353431536	50	51
>chr16	90354753	2458013563	50	51
>chr17	81195210	2550175419	50	51
>chr18	78077248	2632994541	50	51
>chr19	59128983	2712633341	50	51
>chr20	63025520	2772944911	50	51
>chr21	48129895	2837230949	50	51
>chr22	51304566	2886323449	50	51
>chrX	155270560	2938654113	50	51
>chrY	59373566	3097030091	50	51
>chrM	16571	3157591135	50	51
>
>Bam header:
>@HD	VN:1.0	SO:coordinate
>@SQ	SN:chr20	LN:62940766	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr21	LN:48129227	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr22	LN:51253224	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr5	LN:180910700	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr6	LN:170933915	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr7	LN:159102511	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr8	LN:146307037	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr9	LN:141156475	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr1	LN:249250020	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr2	LN:243198952	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr3	LN:197957767	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr4	LN:191041935	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr10	LN:135528848	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXA
>daptr
>@SQ	SN:chr11	LN:134900590	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXA
>daptr
>@SQ	SN:chr12	LN:133811418	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXA
>daptr
>@SQ	SN:chr13	LN:115117205	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXA
>daptr
>@SQ	SN:chrY	LN:59014245	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAda
>ptr
>@SQ	SN:chrX	LN:155267065	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr15	LN:102530814	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXA
>daptr
>@SQ	SN:chr14	LN:107295415	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXA
>daptr
>@SQ	SN:chr17	LN:81198313	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr16	LN:90291808	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr19	LN:59126095	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chr18	LN:78015294	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAd
>aptr
>@SQ	SN:chrM	LN:26571	AS:AS:hgEnsTransRad46Num100kMin10SplicesChrPhiXAdaptr
>@RG	ID:unknownReadGroup	SM:unknownSample
>@PG	ID:SamTranscriptomeParser	CL: args -f
>9657X1_121116_SN141_0600_AD1FYUACXX_1.sam.gz
>
>thanks for your input,
>Jesse Rowley
>Division of Pulmonary Medicine
>University of Utah School of Medicine