Two y chromosome Ensembl 63?

[fabrice]

I used Ensembl 63 DNA as the reference genome: Homo_sapiens.GRCh37.63.dna.chromosome.fa. When mapping my reads using BWA, I found two Y chromosomes. It seems to me that samtools sort cannot work correct on this mapping.

samtools view -H bwa890.bam
@SQ SN:MT LN:16569
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:19 LN:59128983
@SQ SN:Y LN:59373566
@SQ SN:Y LN:59373566
@SQ SN:20 LN:63025520
@SQ SN:18 LN:78077248
@SQ SN:17 LN:81195210
@SQ SN:16 LN:90354753
@SQ SN:15 LN:102531392
@SQ SN:14 LN:107349540
@SQ SN:13 LN:115169878
@SQ SN:12 LN:133851895
@SQ SN:11 LN:135006516
@SQ SN:10 LN:135534747
@SQ SN:9 LN:141213431
@SQ SN:8 LN:146364022
@SQ SN:X LN:155270560
@SQ SN:7 LN:159138663
@SQ SN:6 LN:171115067
@SQ SN:5 LN:180915260
@SQ SN:4 LN:191154276
@SQ SN:3 LN:198022430
@SQ SN:2 LN:243199373
@SQ SN:1 LN:249250621
@PG ID:bwa PN:bwa VN:0.5.9-r16


awk '{if($0 ~/dna:chromosome/)print}' Homo_sapiens.GRCh37.63.dna.chromosome.fa

>MT dna:chromosome chromosome:GRCh37:MT:1:16569:1
>21 dna:chromosome chromosome:GRCh37:21:1:48129895:1
>22 dna:chromosome chromosome:GRCh37:22:1:51304566:1
>19 dna:chromosome chromosome:GRCh37:19:1:59128983:1
>Y dna:chromosome chromosome:GRCh37:Y:1:10000:1
>Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1
>20 dna:chromosome chromosome:GRCh37:20:1:63025520:1
>18 dna:chromosome chromosome:GRCh37:18:1:78077248:1
>17 dna:chromosome chromosome:GRCh37:17:1:81195210:1
>16 dna:chromosome chromosome:GRCh37:16:1:90354753:1
>15 dna:chromosome chromosome:GRCh37:15:1:102531392:1
>14 dna:chromosome chromosome:GRCh37:14:1:107349540:1
>13 dna:chromosome chromosome:GRCh37:13:1:115169878:1
>12 dna:chromosome chromosome:GRCh37:12:1:133851895:1
>11 dna:chromosome chromosome:GRCh37:11:1:135006516:1
>10 dna:chromosome chromosome:GRCh37:10:1:135534747:1
>9 dna:chromosome chromosome:GRCh37:9:1:141213431:1
>8 dna:chromosome chromosome:GRCh37:8:1:146364022:1
>X dna:chromosome chromosome:GRCh37:X:1:155270560:1
>7 dna:chromosome chromosome:GRCh37:7:1:159138663:1
>6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
>5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
>4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
>3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
>2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1

[fabrice]

just replace the header?