FixVcfMissingGenotypes can't find bams

[arundurvasula]

FixVcfMissingGenotypes can't find bams

[lindenb]

I don't see any error in the log you show, just logs/info

But are you sure the BAM contains the name of the sample in the header ?

show me a BAM header please and the CHROM line of the VCF

[arundurvasula]

Actually it's a warning, not an error. But it looks like it doesn't fill in any missing genotypes. Here's the output of samtools view -H:

$ samtools view -H M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam
@HD VN:1.4  SO:coordinate
@SQ SN:Chr1 LN:30427671
@SQ SN:Chr2 LN:19698289
@SQ SN:Chr3 LN:23459830
@SQ SN:Chr4 LN:18585056
@SQ SN:Chr5 LN:26975502
@SQ SN:chloroplast  LN:154478
@SQ SN:mitochondria LN:366924
@SQ SN:hapAC    LN:24696
@SQ SN:hapB LN:56105
@SQ SN:hapC LN:117359
@SQ SN:Ah03_C1  LN:12888
@SQ SN:Ah03_C2  LN:1223
@SQ SN:Ah03_C4  LN:3955
@SQ SN:Ah03_C5  LN:19265
@SQ SN:Ah03_C6  LN:5565
@SQ SN:Ah03_C8  LN:925
@SQ SN:Ah13_C1  LN:46029
@SQ SN:Ah13_C2  LN:1107
@SQ SN:Ah13_C3  LN:2137
@SQ SN:Ah13_C4  LN:13423
@SQ SN:Ah15_Ca1 LN:36209
@SQ SN:Ah15_Ca2 LN:9297
@SQ SN:Ah15_Ca3 LN:6049
@SQ SN:Ah15_Ca5 LN:26447
@SQ SN:Ah15_Ca6 LN:3026
@SQ SN:Ah15_Ca7 LN:6503
@SQ SN:Ah15_Ca8 LN:4372
@SQ SN:Ah15_Ca9 LN:6828
@SQ SN:Ah15_Cu2 LN:2968
@SQ SN:Ah15_Cu3 LN:26001
@SQ SN:Ah15_Cu4 LN:14428
@SQ SN:Ah20_C2  LN:28216
@SQ SN:Ah20_C3  LN:6401
@SQ SN:Ah20_C4  LN:4409
@SQ SN:Ah32_C1  LN:24522
@SQ SN:Ah32_C3  LN:2507
@SQ SN:Ah32_C4  LN:15146
@SQ SN:CapsellaRubella  LN:72853
@SQ SN:lyrata_S16   LN:99048
@SQ SN:lyrata_S38   LN:85472
@SQ SN:lyrata_S50   LN:115380
@SQ SN:lyrata_Sb    LN:116781
@SQ SN:Ah03C3_embl  LN:12754
@SQ SN:Ah13C5_embl  LN:25196
@SQ SN:Ah15Ca4_embl LN:9812
@SQ SN:Ah15Cu1_embl LN:41660
@SQ SN:Ah20C1_embl  LN:42542
@SQ SN:Ah28U1_embl  LN:68975
@SQ SN:Ah28U2_embl  LN:32554
@SQ SN:Ah28Ca1_embl LN:63904
@SQ SN:Ah28Ca3_embl LN:17474
@SQ SN:Ah32C2_embl  LN:25079
@SQ SN:Ah32C5_embl  LN:47589
@SQ SN:Ah43C3_embl  LN:3150
@SQ SN:Ah43C4_embl  LN:829
@SQ SN:Ah43C5_embl  LN:34958
@SQ SN:Ah43C6_embl  LN:5206
@SQ SN:Ah43C7_embl  LN:36265
@SQ SN:Ah43C8_embl  LN:4856
@SQ SN:Al01C1_embl  LN:50758
@SQ SN:Al01C2_embl  LN:30867
@SQ SN:Al14C1_embl  LN:71234
@SQ SN:Al14C2_embl  LN:23881
@SQ SN:Al18Ca1_embl LN:48782
@SQ SN:Al18Ca2_embl LN:23297
@SQ SN:Al18Ca3_embl LN:18188
@SQ SN:Al18Cu1_embl LN:21997
@SQ SN:Al18Cu2_embl LN:39655
@SQ SN:Al39C1_embl  LN:12578
@SQ SN:Al39C2_embl  LN:3366
@SQ SN:Al39C3_embl  LN:18739
@SQ SN:Al39C4_embl  LN:32763
@SQ SN:Al39C5_embl  LN:22614
@SQ SN:AhSRK12_EU075133.1   LN:260
@SQ SN:AhSRK21_EU075142.1   LN:260
@SQ SN:AhSRK27_EU878012.1   LN:260
@SQ SN:AkSRKD   LN:260
@SQ SN:AlSRK02_AY186763.1   LN:260
@SQ SN:AlSRK07_AY186765.1   LN:260
@SQ SN:AlSRK15_AY186771.1   LN:260
@SQ SN:AlSRK23_AF328997.2   LN:260
@SQ SN:AlSRK35_EU878021.1   LN:260
@SQ SN:AlSRK45_EU878026.1   LN:260
@PG ID:bwa  PN:bwa  VN:0.7.5a-r405
@PG ID:MarkDuplicates   PN:MarkDuplicates   VN:1.100(1571)  CL:net.sf.picard.sam.MarkDuplicates INPUT=[/scratch/myCallsIntermediate/22010/M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam] OUTPUT=/scratch/myCallsIntermediate/22010/M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam METRICS_FILE=pe.dupstat.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false

And the vcf line:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  M-Ait14.22010_CAAGACTA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam  M-Ait9.22003_GTCTGTCA_C5E9DANXX_6_20140930B_20140930.bam.sam.sortP.sam.duprem.sam.bam

[lindenb]

There is no @rg group in your BAM.
See the SAM spec and http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups