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I know that there is a lot of methods to do so, but most of them need to have a reference file. (For example, the GATK force me to provide a reference.) However, I think the BAM file I am working with already embedded the reference information in it. I tried to use the Samtool (mpileup) to do that, but it seems that the vcf file I get has different formats compared with the VCF documentations. Could anyone give me some advice?

Also, could anyone provide a method to validate the vcf file without using a reference file?

Thanks a lot! The following is what I got when running:

samtools view -H

@HD VN:1.5  GO:none SO:coordinate
@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717
@SQ SN:chr10    LN:133797422
@SQ SN:chr11    LN:135086622
@SQ SN:chr12    LN:133275309
@SQ SN:chr13    LN:114364328
@SQ SN:chr14    LN:107043718
@SQ SN:chr15    LN:101991189
@SQ SN:chr16    LN:90338345
@SQ SN:chr17    LN:83257441
@SQ SN:chr18    LN:80373285
@SQ SN:chr19    LN:58617616
@SQ SN:chr20    LN:64444167
@SQ SN:chr21    LN:46709983
@SQ SN:chr22    LN:50818468
@SQ SN:chrX LN:156040895
@SQ SN:chrY LN:57227415
@SQ SN:chrM LN:16569
@SQ SN:chr1_KI270706v1_random   LN:175055
@SQ SN:chr1_KI270707v1_random   LN:32032
@SQ SN:chr1_KI270708v1_random   LN:127682
@SQ SN:chr1_KI270709v1_random   LN:66860
@SQ SN:chr1_KI270710v1_random   LN:40176
@SQ SN:chr1_KI270711v1_random   LN:42210
@SQ SN:chr1_KI270712v1_random   LN:176043
@SQ SN:chr1_KI270713v1_random   LN:40745
@SQ SN:chr1_KI270714v1_random   LN:41717
@SQ SN:chr2_KI270715v1_random   LN:161471
@SQ SN:chr2_KI270716v1_random   LN:153799
@SQ SN:chr3_GL000221v1_random   LN:155397
@SQ SN:chr4_GL000008v2_random   LN:209709
@SQ SN:chr5_GL000208v1_random   LN:92689
@SQ SN:chr9_KI270717v1_random   LN:40062
@SQ SN:chr9_KI270718v1_random   LN:38054
@SQ SN:chr9_KI270719v1_random   LN:176845
@SQ SN:chr9_KI270720v1_random   LN:39050
@SQ SN:chr11_KI270721v1_random  LN:100316
@SQ SN:chr14_GL000009v2_random  LN:201709
@SQ SN:chr14_GL000225v1_random  LN:211173
@SQ SN:chr14_KI270722v1_random  LN:194050
@SQ SN:chr14_GL000194v1_random  LN:191469
@SQ SN:chr14_KI270723v1_random  LN:38115
@SQ SN:chr14_KI270724v1_random  LN:39555
@SQ SN:chr14_KI270725v1_random  LN:172810
@SQ SN:chr14_KI270726v1_random  LN:43739
@SQ SN:chr15_KI270727v1_random  LN:448248
@SQ SN:chr16_KI270728v1_random  LN:1872759
@SQ SN:chr17_GL000205v2_random  LN:185591
@SQ SN:chr17_KI270729v1_random  LN:280839
@SQ SN:chr17_KI270730v1_random  LN:112551
@SQ SN:chr22_KI270731v1_random  LN:150754
@SQ SN:chr22_KI270732v1_random  LN:41543
@SQ SN:chr22_KI270733v1_random  LN:179772
@SQ SN:chr22_KI270734v1_random  LN:165050
@SQ SN:chr22_KI270735v1_random  LN:42811
@SQ SN:chr22_KI270736v1_random  LN:181920
@SQ SN:chr22_KI270737v1_random  LN:103838
@SQ SN:chr22_KI270738v1_random  LN:99375
@SQ SN:chr22_KI270739v1_random  LN:73985
@SQ SN:chrY_KI270740v1_random   LN:37240
@SQ SN:chrUn_KI270302v1 LN:2274
@SQ SN:chrUn_KI270304v1 LN:2165
@SQ SN:chrUn_KI270303v1 LN:1942
@SQ SN:chrUn_KI270305v1 LN:1472
@SQ SN:chrUn_KI270322v1 LN:21476
@SQ SN:chrUn_KI270320v1 LN:4416
@SQ SN:chrUn_KI270310v1 LN:1201
@SQ SN:chrUn_KI270316v1 LN:1444
@SQ SN:chrUn_KI270315v1 LN:2276
@SQ SN:chrUn_KI270312v1 LN:998
@SQ SN:chrUn_KI270311v1 LN:12399
@SQ SN:chrUn_KI270317v1 LN:37690
@SQ SN:chrUn_KI270412v1 LN:1179
@SQ SN:chrUn_KI270411v1 LN:2646
@SQ SN:chrUn_KI270414v1 LN:2489
@SQ SN:chrUn_KI270419v1 LN:1029
@SQ SN:chrUn_KI270418v1 LN:2145
@SQ SN:chrUn_KI270420v1 LN:2321
@SQ SN:chrUn_KI270424v1 LN:2140
@SQ SN:chrUn_KI270417v1 LN:2043
@SQ SN:chrUn_KI270422v1 LN:1445
@SQ SN:chrUn_KI270423v1 LN:981
@SQ SN:chrUn_KI270425v1 LN:1884
@SQ SN:chrUn_KI270429v1 LN:1361
@SQ SN:chrUn_KI270442v1 LN:392061
@SQ SN:chrUn_KI270466v1 LN:1233
@SQ SN:chrUn_KI270465v1 LN:1774
@SQ SN:chrUn_KI270467v1 LN:3920
@SQ SN:chrUn_KI270435v1 LN:92983
@SQ SN:chrUn_KI270438v1 LN:112505
@SQ SN:chrUn_KI270468v1 LN:4055
@SQ SN:chrUn_KI270510v1 LN:2415
@SQ SN:chrUn_KI270509v1 LN:2318
@SQ SN:chrUn_KI270518v1 LN:2186
@SQ SN:chrUn_KI270508v1 LN:1951
@SQ SN:chrUn_KI270516v1 LN:1300
@SQ SN:chrUn_KI270512v1 LN:22689
@SQ SN:chrUn_KI270519v1 LN:138126
@SQ SN:chrUn_KI270522v1 LN:5674
@SQ SN:chrUn_KI270511v1 LN:8127
@SQ SN:chrUn_KI270515v1 LN:6361
@SQ SN:chrUn_KI270507v1 LN:5353
@SQ SN:chrUn_KI270517v1 LN:3253
@SQ SN:chrUn_KI270529v1 LN:1899
@SQ SN:chrUn_KI270528v1 LN:2983
@SQ SN:chrUn_KI270530v1 LN:2168
@SQ SN:chrUn_KI270539v1 LN:993
@SQ SN:chrUn_KI270538v1 LN:91309
@SQ SN:chrUn_KI270544v1 LN:1202
@SQ SN:chrUn_KI270548v1 LN:1599
@SQ SN:chrUn_KI270583v1 LN:1400
@SQ SN:chrUn_KI270587v1 LN:2969
@SQ SN:chrUn_KI270580v1 LN:1553
@SQ SN:chrUn_KI270581v1 LN:7046
@SQ SN:chrUn_KI270579v1 LN:31033
@SQ SN:chrUn_KI270589v1 LN:44474
@SQ SN:chrUn_KI270590v1 LN:4685
@SQ SN:chrUn_KI270584v1 LN:4513
@SQ SN:chrUn_KI270582v1 LN:6504
@SQ SN:chrUn_KI270588v1 LN:6158
@SQ SN:chrUn_KI270593v1 LN:3041
@SQ SN:chrUn_KI270591v1 LN:5796
@SQ SN:chrUn_KI270330v1 LN:1652
@SQ SN:chrUn_KI270329v1 LN:1040
@SQ SN:chrUn_KI270334v1 LN:1368
@SQ SN:chrUn_KI270333v1 LN:2699
@SQ SN:chrUn_KI270335v1 LN:1048
@SQ SN:chrUn_KI270338v1 LN:1428
@SQ SN:chrUn_KI270340v1 LN:1428
@SQ SN:chrUn_KI270336v1 LN:1026
@SQ SN:chrUn_KI270337v1 LN:1121
@SQ SN:chrUn_KI270363v1 LN:1803
@SQ SN:chrUn_KI270364v1 LN:2855
@SQ SN:chrUn_KI270362v1 LN:3530
@SQ SN:chrUn_KI270366v1 LN:8320
@SQ SN:chrUn_KI270378v1 LN:1048
@SQ SN:chrUn_KI270379v1 LN:1045
@SQ SN:chrUn_KI270389v1 LN:1298
@SQ SN:chrUn_KI270390v1 LN:2387
@SQ SN:chrUn_KI270387v1 LN:1537
@SQ SN:chrUn_KI270395v1 LN:1143
@SQ SN:chrUn_KI270396v1 LN:1880
@SQ SN:chrUn_KI270388v1 LN:1216
@SQ SN:chrUn_KI270394v1 LN:970
@SQ SN:chrUn_KI270386v1 LN:1788
@SQ SN:chrUn_KI270391v1 LN:1484
@SQ SN:chrUn_KI270383v1 LN:1750
@SQ SN:chrUn_KI270393v1 LN:1308
@SQ SN:chrUn_KI270384v1 LN:1658
@SQ SN:chrUn_KI270392v1 LN:971
@SQ SN:chrUn_KI270381v1 LN:1930
@SQ SN:chrUn_KI270385v1 LN:990
@SQ SN:chrUn_KI270382v1 LN:4215
@SQ SN:chrUn_KI270376v1 LN:1136
@SQ SN:chrUn_KI270374v1 LN:2656
@SQ SN:chrUn_KI270372v1 LN:1650
@SQ SN:chrUn_KI270373v1 LN:1451
@SQ SN:chrUn_KI270375v1 LN:2378
@SQ SN:chrUn_KI270371v1 LN:2805
@SQ SN:chrUn_KI270448v1 LN:7992
@SQ SN:chrUn_KI270521v1 LN:7642
@SQ SN:chrUn_GL000195v1 LN:182896
@SQ SN:chrUn_GL000219v1 LN:179198
@SQ SN:chrUn_GL000220v1 LN:161802
@SQ SN:chrUn_GL000224v1 LN:179693
@SQ SN:chrUn_KI270741v1 LN:157432
@SQ SN:chrUn_GL000226v1 LN:15008
@SQ SN:chrUn_GL000213v1 LN:164239
@SQ SN:chrUn_KI270743v1 LN:210658
@SQ SN:chrUn_KI270744v1 LN:168472
@SQ SN:chrUn_KI270745v1 LN:41891
@SQ SN:chrUn_KI270746v1 LN:66486
@SQ SN:chrUn_KI270747v1 LN:198735
@SQ SN:chrUn_KI270748v1 LN:93321
@SQ SN:chrUn_KI270749v1 LN:158759
@SQ SN:chrUn_KI270750v1 LN:148850
@SQ SN:chrUn_KI270751v1 LN:150742
@SQ SN:chrUn_KI270752v1 LN:27745
@SQ SN:chrUn_KI270753v1 LN:62944
@SQ SN:chrUn_KI270754v1 LN:40191
@SQ SN:chrUn_KI270755v1 LN:36723
@SQ SN:chrUn_KI270756v1 LN:79590
@SQ SN:chrUn_KI270757v1 LN:71251
@SQ SN:chrUn_GL000214v1 LN:137718
@SQ SN:chrUn_KI270742v1 LN:186739
@SQ SN:chrUn_GL000216v2 LN:176608
@SQ SN:chrUn_GL000218v1 LN:161147
@SQ SN:chrEBV   LN:171823
@RG ID:Wit_Exon9_DEL_FKDN202385493-1A_H5HHJDSXY_L1  CN:Novogene LB:Wit_Exon9_DEL    PL:illuminPU:Wit_Exon9_DEL_FKDN202385493-1A_H5HHJDSXY_L1    SM:Wit_Exon9_DEL
@PG ID:bwa  PN:bwa  CL:bwa mem -t 8 -M -R @RG\tID:Wit_Exon9_DEL_FKDN202385493-1A_H5HHJDSXY_L1\tSM:Wit_Exon9_DEL\tLB:Wit_Exon9_DEL\tPU:Wit_Exon9_DEL_FKDN202385493-1A_H5HHJDSXY_L1\tPL:illumina\tCN:Novogene /PUBLIC/source/HW/Disease/database/genome/human/hg38/bwa_index_whole/hg38.fa /TJPROJ6/GB_HUMAN/PJ_AI/cancer/auto-WES-Somatic/1000/X202SC2005/X202SC20050050-Z01/F002/QC/Wit_Exon9_DEL/Wit_Exon9_DEL_FKDN202385493-1A_H5HHJDSXY_L1_1.clean.fq.gz /TJPROJ6/GB_HUMAN/PJ_AI/cancer/auto-WES-Somatic/1000/X202SC2005/X202SC20050050-Z01/F002/QC/Wit_Exon9_DEL/Wit_Exon9_DEL_FKDN202385493-1A_H5HHJDSXY_L1_2.clean.fq.gz  VN:0.7.17-r1188
@PG ID:sambamba CL:view -S -f bam /dev/stdin    PP:bwa  VN:1.0
@PG ID:MarkDuplicates   VN:2.18.9-SNAPSHOT  CL:MarkDuplicates INPUT=[/TJPROJ6/GB_HUMAN/PJ_AI/service/cromwell/cromwell-executions/ToSomatic/fddd223f-25fd-4533-ae86-14e106c58ec5/call-Mapping/shard-0/Mapping/14f30bea-add3-4ead-b7e1-fcb202ae18f5/call-picardMarkdup/inputs/-714370009/Wit_Exon9_DEL.merge.bam] OUTPUT=/TJPROJ6/GB_HUMAN/PJ_AI/cancer/auto-WES-Somatic/1000/X202SC2005/X202SC20050050-Z01/F002/Mapping/Wit_Exon9_DEL/Wit_Exon9_DEL.final.bam METRICS_FILE=metric.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[.] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=4000000 CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   PN:MarkDuplicates
@PG ID:samtools PN:samtools PP:sambamba VN:1.10 CL:samtools view -H /Users/XXXX/Desktop/data/02.Bam/XXXX.final.bam
@PG ID:samtools.1   PN:samtools PP:MarkDuplicates   VN:1.10 CL:samtools view -H /Users/XXXX/Desktop/data/02.Bam/XXXX.final.bam

The output file I get when using Samtools looks like: enter image description here

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5
  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Feb 16, 2022 at 18:44
  • $\begingroup$ In my experience, BAM files don't have the reference sequence in them - CRAM files can. On what basis do you think your BAM has the reference "embedded in it"? $\endgroup$
    – Ram RS
    Feb 16, 2022 at 20:05
  • $\begingroup$ This is a very broad question, please try and make a clear effort to narrow down what you are requesting. $\endgroup$
    – M__ ♦
    Feb 16, 2022 at 21:58
  • $\begingroup$ is the reference sequence mentioned as a metadata tag in the BAM file header? Can you show the output of samtools view -H myBamFile.bam? (which will only show the header information) $\endgroup$
    – gringer ♦
    Feb 17, 2022 at 21:14
  • $\begingroup$ When I use the samtools to get the vcf file, the output file is incorrect (miss a lot of columns). That is the main reasons why I ask this question here. Also, if a reference file is needed, how/where could I get it? Can I just download the general reference file from the gatk website, or a specific/ project-related reference file is needed? $\endgroup$
    – Scott XU
    Feb 21, 2022 at 21:39

2 Answers 2

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To go from .bam to .vcf, it is fairly easy using bcftools call:

bcftools mpileup -Ob -o <study.bcf> -f <ref.fa> <sample1.bam> 
bcftools call -vmO z -o <study.vcf.gz> <study.bcf>

Taken from htslib website.

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3
  • $\begingroup$ Does this method is applicable when I only have BAM files without bcf files? $\endgroup$
    – Scott XU
    Feb 23, 2022 at 17:39
  • $\begingroup$ @scott - the bcf (it’s the same as a vcf) is the output, not the input, so you’re fine to use it. $\endgroup$
    – user438383
    Feb 23, 2022 at 18:00
  • $\begingroup$ Hi~~ When I actually tried this method, I get some output like [E::faidx_adjust_position] The sequence "chr1_KI270706v1_random" was not found. Do you know how to fix it? Thanks a lot~~~ $\endgroup$
    – Scott XU
    Feb 23, 2022 at 21:31
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Recently, I also had a similar question and got my answer from Biostars. See my post and the answer I received: Germline variant calling from BAM without reference.

Basically, I was also wondering if it is possible to call SNVs/indels from aligned BAM files without reference because reference sequence was already used to produce such files. To this end, it appears some BAM files contain useful (but optional) read-level tags such as MD which, if present, would allow one to even reconstruct the entire reference sequence. For more details, please visit the link above.

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